Stokes, who trailed Holder by 54 rating points going into the second Test in Manchester, enjoys a lead of 38 points after his memorable knocks of 176 and 78 not out and a match haul of three wickets helped England win by 113 runs and level the three-match series 1-1.
Ben Stokes vs Jason Holder
Stokes ended Holder's 18-month reign at the top, becoming the first from England at the summit since Andrew Flintoff in May 2006. His tally of 497 rating points is the highest by any Test all-rounder since Jacques Kallis aggregated 517 in April 2008.
ICC Test all-rounders rankings
India's Ravindra Jadeja remains in third spot with Australian Mitchell Starc and Ravichandran Ashwin rounding up the top-five.
ICC Test batsmen rankings
Among batsmen, Stokes is joint-third with Marnus Labuschagne, only behind Steve Smith
and India skipper Virat Kohli, with specialist batsmen like Kane Williamson
and Babar Azam below him in the list. His captain Joe Root is ninth while opener Dom Sibley has advanced 29 places to a career-best 35th position after a sturdy first innings 120.
Cheteshwar Pujara and Ajinkya Rahane have a dropped a spot each to be eighth and 10th respectively, having not played since March due to the Covid-19 pandemic.
ICC Test rankings: Bowlers
Stuart Broad, who was not picked for the opening Test, returned to the top 10 of the bowlers' rankings after claiming three wickets in each innings.
He is now England's top-ranked bowler, one slot ahead of James Anderson, who dropped to 11th after being rested for the match. Chris Woakes, who scalped five in the match to reach the 100-wicket mark, is in 21st position, his highest since late 2016.
ICC Test Rankings: West Indian players
For the West Indies, Shamarh Brooks has moved up 27 places to a career-best 45th position after scores of 68 and 62. He is now just four slots behind Holder, who remains the top-ranked West Indies batsman in 41st position despite slipping four places.
Holder has also dropped a slot among bowlers to take third place, behind Pat Cummins and Neil Wagner.
Roston Chase has gained two places in the bowlers' list after a five-wicket haul in the first innings.
ICC World Test Championship:
The win at Old Trafford has lifted England to third position in the points table. They are now on 186 points, six more than New Zealand. Check Test Championship points table here
India leads with 360 points while Australia is second at 296. The West Indies remain on 40 points.
Each series of the WTC is worth 120 points, distributed evenly over the number of matches in a series. The points range from 60 for each match of a two-Test series to 24 for each match of a five-Test series.