Long broke the deadlock after just 7.69 seconds - beating the previous record of 9.82 seconds set by Ledley King nearly 20 years ago - but the Hornets salvaged a point as Andre Gray netted an equaliser in the 90th minute.
Long set the new record as he blocked a Craig Cathcart pass before lifting the ball over Ben Foster in the Watford goal.
That early strike appeared to have settled matters until the closing stages when Gray scored from close range thanks to Daryl Janmaat's assist.
The point edges Southampton closer to safety as they are now six points clear of Cardiff in 18th spot with just three games left to play.
Watford move ahead of Everton and into seventh spot as the Hornets continue their battle for Europa League football next season.