Colin Nish chipped in the opener after a dreadful mistake from Buddies goalkeeper Chris Smith, and Merouane Zemmama drove in a second barely 90 seconds later.
With Steven Fletcher’s 12th-minute header also ruled out for offside, it looked like being a comfortable afternoon for the Easter Road outfit.
But the visitors bossed the match thereafter and Andrew McNeil had to make vital saves from Will Haining and Stewart Kean late on to make sure of the three points.
The win for Hibernian carries them above Dundee United into fourth place in the Scottish Premier League, a point above the Terrors having played a game more.
St Mirren stay 11th, a point behind Kilmarnock with two games in hand.