Boss Gareth Southgate made five changes to the Three Lions’ starting XI which thrashed Montenegro 7-0 at Wembley on Thursday. Raheem Sterling returned to the side, Burnley goalkeeper Nick Pope was handed his first start, while Tyrone Mings, Declan Rice and Callum Hudson-Odoi also came in.
Kosovo coach Bernard Challandes made one change from the side that lost 2-1 to the Czech Republic last Thursday as Heerenveen defender Ibrahim Dresevic replaced Anel Rashkaj.
England qualified as group winners thanks to the mauling of Montenegro but were looking to end their qualification campaign on a winning note.
It took until the 16th minute for them to generate a first serious attempt on the Kosovo goal when Ben Chilwell surged down the left and put in a cross which Harry Kane laid into the path of Sterling, but his right-foot strike was parried wide by Arijanet Muric.
Kosovo enjoyed a decent spell with Milot Rashica testing Pope, before Benjamin Kololli sent an effort from outside of the area sailing over the top of the goal.
England issued a response through Hudson-Odoi on the half-hour but his strike from inside the area was straight at Muric.
The Three Lions did get their noses in front on 32 minutes when Alex Oxlade-Chamberlain picked out the run of Winks and he raced into the area before beating Muric with an effort into the bottom corner to secure his first international goal.
England failed to build on their lead and it was Kosovo who again went close five minutes into the second half. A corner was only half-cleared to Valon Berisha on the edge of the box and his strike was flicked on by Amir Rrahmani as the ball rolled inches wide of Pope’s far corner.
Rrahmani should have done better on 52 minutes when he was unmarked as he got on the end of a Berisha cross from the right, but he made a complete hash of his header, sending it well wide.
England finally woke up and were inches away from doubling their advantage on 62 minutes when Muric could only parry a Chilwell effort and Sterling pounced on the loose ball to set up Kane, but his strike rebounded off the post.
The Three Lions wrapped up the win 11 minutes from time when a Sterling cross from the right was inadvertently sent towards the back post by a poor defensive clearance and Kane was on hand to volley in his 12th goal of the qualification campaign.
Substitute Marcus Rashford made it 3-0 on 83 minutes when he stroked home a first-time shot past Muric from the left of area after being teed up by Sterling.
Substitute Mason Mount put the icing on the cake in stoppage time with his first Three Lions’ goal after being set up by Kane inside the area.
England finish top of the pile with 21 points from a possible 24, the Czech Republic also qualify in second place, while Kosovo will get another chance via the play-offs.