With regular captain Joe Root watching from home with his new baby, Isabella, the home side were bowled out for 204 in tricky conditions that must have made stand-in skipper Ben Stokes question his own wisdom in batting first.
While the heavy grey clouds and permanent floodlights did not help, Holder and Shannon Gabriel, who took four for 62, exploited them wonderfully.
Stokes' 43 was the best his team could muster in response but even that required two drops in the outfield.
Much had been made of the head-to-head battle between the rival all-rounders and Holder's brilliance went a long towards explaining why he sits atop the International Cricket Council's rankings.
A rain-affected start to the series saw England resuming on 35 for one and they never managed to get their noses in front as they subsided in 67.3 overs.
Gabriel, who claimed the only success of day one, gave the Windies a perfect start with two more early breakthroughs in the morning session. His first was Joe Denly, who spent 27 minutes scoring his first runs of the day and was clean bowled between bat and pad from the very next ball.
His knock of 18 from 58 will do little to ease the scrutiny over his place, but his struggles were hardly out of place.
Gabriel followed up by seeing off Rory Burns, who had looked solid for 30 before playing across a fast yorker that was destined for leg stump. Richard Kettleborough rejected the initial appeal but DRS settled the matter in Gabriel's favour.
From there on it was all about Holder, the highest ranked bowler on either side at number three in the world.
He opened his account with Zak Crawley, effectively auditioning to replace Kent team-mate Denly at number three when Root returns. As before Kettleborough rejected the lbw appeal and, as before, replays over-ruled him.
Holder yielded back-to-back boundaries off new man Ollie Pope but was quick to respond, drawing a loose prod in the channel and having the Surrey batsman caught for 12.
England's lunch score of 106 for five would have been worse had Kemar Roach held a tough chance at fine leg off Stokes' top-edge but the ball slipped loose. For a spell after lunch that looked to be a costly miss, as Stokes and Jos Buttler made a dashing stand of 67.
There was a second life for Stokes – put down horribly by Shamarh Brooks at short cover on 32 – but also a series of sweet strokes. Both launched Gabriel to the cover-point boundary in the first over of the session, the first of several to follow.
It was Holder who sent both men back in a spell of guile and unflinching accuracy. Stokes nicked behind compulsively advancing down the pitch and, just seven balls later, Buttler (35) was brilliantly held one-handed by wicketkeeper Shane Dowrich.
He made it five when Jofra Archer was lbw for a duck, DRS to the rescue for the third time, and Mark Wood was caught at gully to make it six. Dom Bess (31no) led a useful last-wicket stand of 30 before Gabriel sent James Anderson packing.