Captain Ryan ten Doeschate's 88 took Essex from 188-8 to 231 all out before lunch - a first-innings lead of 118.
A second superb spell of pace bowling in the match from Mohammad Amir (5-54) then saw Yorkshire bowled out for 150, and Essex eased to 34-2 for victory.
Essex now lead second-placed Lancashire by 49 points with five games left.
The Red Rose county are currently playing third-placed Hampshire at the Ageas Bowl and host Essex in what could be a pivotal match at the start of September.
Pakistan paceman Amir was unplayable at times on a seamer-friendly pitch at Scarborough, finishing with career-best match figures of 10-72.
Four Yorkshire batsmen were out for nought, including opener Alex Lees who edged Amir behind to register a pair, while Jack Leaning fought with a gritty 70 before he was last man out to Jamie Porter (4-41).
Essex lost openers Varun Chopra and Nick Browne in their small chase, but it mattered little as they picked up their sixth win in nine games.
Yorkshire, champions in 2014 and 2015, have now lost four out of 10 matches this summer, with several of their batsmen averaging less than 30.
Essex, who were promoted from Division Two last season, won the last of their six County Championship crowns in 1992 under Graham Gooch.
Unbeaten Division One leaders Essex thumped Yorkshire inside two days to strengthen their bid for a first County Championship title in 25 years.