Strikes from Ryan Watson, Callum Morton, Sam Hoskins and substitute Andy Williams earned the Cobblers a resounding win in the behind-closed-doors clash.
Toothless Exeter were second best throughout the contest and endured another miserable trip to the capital, losing this winner-takes-all fixture for the third time in four seasons.
The Grecians, beaten by Blackpool in 2017 and Coventry in 2018, ended the contest with 10 men after Dean Moxey was shown a second-half red card for lunging at Watson with the score 2-0.
Victory for Town ended their two-year exile from the third tier, while earning manager Keith Curle a maiden promotion of a managerial career which began in 2002.
They will join fellow promoted sides Swindon, Crewe and Plymouth in League One next season.
The teams took to an immaculate-looking pitch 331 days after the start of the League Two season and on the day the cancelled Wimbledon tennis championships were scheduled to begin.
After British soprano Faryl Smith contributed to the surreal atmosphere by performing a pre-recorded national anthem on the big screens, the empty 90,000-seater stadium fell completely silent in memory of Theo Foley.
Irishman Foley, who died on Friday aged 83, had connections to both clubs, captaining and managing Northampton after beginning his professional career with Exeter.
Supporters, absent due to coronavirus restrictions, were partly replaced by a host of cardboard cut-outs, with NBA great Shaquille O’Neal and comedian Alan Carr among Northampton’s celebrity backers and Coldplay frontman Chris Martin and actor Adrian Edmondson in the Exeter end.
Town began brighter and took an 11th-minute lead with the game’s first attempt at goal.
After Charlie Goode’s long throw was partially cleared to the edge of the box, Watson calmly sidestepped City skipper Jake Taylor before his low left-footed strike took a slight deflection off Aaron Martin and flew into the bottom right corner.
Exeter had finished seven points above their opponents in the curtailed regular season but they were left with an uphill battle following static defending in the 31st minute.
Semi-final hero Morton, who scored twice as the Cobblers overturned a 2-0 aggregate deficit against Cheltenham, was left with a simple, close-range volley after Scott Wharton and Jordan Turnbull helped Goode’s searching free-kick across goal.
Grecians boss Matt Taylor had been assistant to Paul Tisdale during Exeter’s previous two play-off final losses.
He was left with his head in his hands following the second goal and his side would have been even further behind at the end of a below-par first-half display had goalkeeper Jonathan Maxted not kept out quickfire stoppage-time headers from Vadaine Oliver and Goode.
Exeter showed little sign of mounting a comeback and their task became even more difficult just before the hour mark when Moxey was shown a straight red card after foolishly sliding in on Watson from behind.
West Brom loanee Morton then wasted a chance to claim his second when he slotted wide when clean through, before Hoksins put the result beyond doubt by coolly slotting in 10 minutes from time after substitute Mark Marshall burst down the right and centred.
Exeter enjoyed more possession but mustered just one attempt on target in the entire contest and their suffering was complete a minute from time when veteran forward Williams hooked home with his first touch after another Goode long throw.
At the end of the game the Northampton players picked up the medals and champagne themselves for social-distancing reasons.
The key talking points ahead of Monday’s League Two play-off final
Exeter and Northampton will battle it out for promotion to League One at an empty Wembley Stadium.
Exeter and Northampton will meet at an empty Wembley Stadium on Monday night in the Sky Bet League Two play-off final.
After the season was curtailed due to the coronavirus pandemic, both will be keen to end an uncertain campaign with promotion to the third tier.
Here, the PA news agency takes a look at some of the biggest talking points ahead of the game.
Can the Grecians earn play-off glory?
This will be Exeter’s third League Two play-off final in four years.
Under Paul Tisdale’s reign on both occasions, their first attempt at a return to League One was ended in 2017 when they lost 2-1 to Blackpool.
Just over a year later and history repeated itself – this time Coventry were the side to get the better of Tisdale’s men, running out comfortable 3-1 winners.
Now it is up to Matt Taylor’s class of 2020 to build on their fifth-place finish and banish recent Wembley woes.
Tayl of success for Exeter boss Matt
The defeat to Coventry saw Tisdale, then the longest-serving manager in English football, depart St James Park after 12 years in charge.
He was replaced by Taylor, a former no-nonsense centre-back embarking on his first foray into management.
Taylor, 38, spent four seasons at Exeter during his career and has enjoyed a decent start to life in the dugout.
A fifth-place finish was enough to secure their play-off berth after the League Two season drew to a close early due to the Covid-19 outbreak and Taylor will be looking to add a promotion to his burgeoning CV.
Wembley provides the biggest empty house since football’s return
The clash will take place in the familiar play-off final venue of Wembley Stadium – but the experience promises to be a unique one.
With the coronavirus pandemic keeping fans away from football, the game at the 90,000-seater national stadium will be played out in front of empty stands.
How the players cope with the eerie silence inside such a huge venue may go some way in deciding who earns promotion on Monday night.
Curle looking for promotion to top first full season at Sixfields
After poor, and short-lived, reigns for both Jimmy Floyd Hasselbaink and Dean Austin, Northampton looked to Keith Curle to turn things around at the club.
The former England defender addressed an alarming slide to keep the club in the English Football League last season following his October appointment.
This year the team have gone from strength to strength and crept into the play-off places, finishing seventh after final standings were decided on a points-per-game basis.
A decent run to the fourth round of the FA Cup also lifted spirits but gaining promotion to League One after two seasons in the fourth tier would be a fine achievement for Curle and his staff.
Cheltenham comeback to inspire turnaround in Cobblers’ pre-lockdown form?
Curle’s side lost five of their last seven league games before the season came to a halt.
That run was punctuated by a 2-0 home win over Exeter back in February, however, and the remarkable semi-final turnaround against Cheltenham should have banished such a run of results.
Cheltenham would have fancied their chances of walking out at Wembley having left Northampton with a 2-0 win in the first leg, but a double from Callum Morton inspired the Cobblers to a 3-0 success at Whaddon Road to keep their own promotion hopes alive.