The West Indies batsman helped his side to victory in the first Test.
Jermaine Blackwood hit a match-winning 95 for the Windies at Southampton.
England are 170 ahead with two tail-end wickets in hand after a frantic final hour on day four.
The captain took four wickets before England closed the day on 15 without loss.
Holder claimed career-best figures of six for 42 to put Ben Stokes’ side under pressure.
The hosts had resumed on 35 for one after a rain-ruined start to the series.
Ben Stokes’ 43 was the best his team could muster in response but even that required two drops in the outfield.
Persistent rain meant only 17 overs were completed before an early tea break.
Both teams took a knee in support of the Black Lives Matter movement before play got under way.
Two minutes’ silence were also observed.