The experienced defender was handed a rare start as Antonio Conte made nine changes compared to the team that clinched the Premier League title against West Brom on Friday and he enjoyed an eventful first half.
Terry opened the scoring in the 22nd minute with a finish from close range, only to inadvertently set up Etienne Capoue for the equaliser with a poor clearance two minutes later.
Cesar Azpilicueta and Michy Batshuayi then struck either side of half-time to hand Chelsea a two-goal lead, only for Daryl Janmaat to pull one back.
Substitute Stefano Okaka seemed to have a salvaged a draw for Watford with 16 minutes left, but it was Fabregas who had the final say, before Sebastian Prodl received his marching orders in added time.
Chelsea are now on 90 points from 37 games ahead of their final game against Sunderland on Sunday, while Watford remain 16th on 40 points.
Both sides made a cautious start to the game, but the champions eventually went ahead midway through the first half via Terry. Kurt Zouma’s header from a corner somewhat fortuitously fell to his defensive partner and Terry was alert to poke the ball past Gomes from close range.