The Buddies had to play almost all of the Scottish Premier League match a man down after midfielder Steven Thomson was red-carded for a wild lunge on former Falkirk team-mate Patrick Cregg.
Despite their disadvantage, the visitors took the lead in the 38th minute when Stephen McGinn capitalised on defensive disarray in the home ranks.
However, the Easter Road men restored parity within 60 seconds as youngster David Wotherspoon side-footed home to set the scene for Benjelloun's winning strike eight minutes from time.
'Benji' spent last season on loan in Belgium and sparked controversy when he tried to engineer a move away from the club in the summer as he refused to return for pre-season training.
However, after arriving back in Edinburgh this week, the Moroccan repaid Hughes' faith in him by earning his manager the perfect start to his new era.
Hibernian, without the injured Merouane Zemmama, made a nervy start before Paul Hanlon saw a header from Cregg's deep cross blocked as they settled in the fifth minute.
Three minutes later, it was the visitors' turn. Michael Higdon's knock-down found Garry Brady on the edge of the area but Ma-Kalambay got down to hold the midfielder's eventual shot.
In the 15th minute, the match exploded to life as St Mirren were reduced to 10 men.
Cregg burst through two stern challenges before being on the receiving end of a two-footed lunge from Thomson, who was given a straight red card by referee Alan Muir.
Despite their man advantage, Hibs were struggling to carve out any meaningful chances and when Derek Riordan did get the ball in the net the referee's whistle had gone long before for a handball against Colin Nish.
Nish then bulleted a header wide from Cregg's cross before the match burst to life again with a goal at either end.
Hibs were the architects of their own downfall as St Mirren took the lead in the 38th minute.
A slack backpass from captain Chris Hogg put Ma-Kalambay under pressure and, after Hanlon had lost the clearance and the keeper had palmed out Andy Dorman's cross, Stephen McGinn was on hand to fire into the unguarded net.
Within a minute, however, Hibs were back on level terms.
John Rankin combined with Riordan and Nish on the edge of the area and the midfielder's ball across the face of goal was side-footed in by youngster Wotherspoon.
St Mirren allowed Hibs easy possession at the start of the second period as they filed every man behind the ball in a bid to make up for being a man down.
However, the tactic was almost ripped apart in the 50th minute when the home side won a corner on the right.
Riordan's delivery was headed towards goal by Bamba but Nish, standing barely three yards from goal, could only redirect the effort on to the crossbar.
Buddies keeper Paul Gallacher held a Riordan shot in the 58th minute and he was called into action again in the 68th minute as Hanlon sent in a powerful drive.
Hughes sent on Benjelloun in place of right-back Kevin McCann with 20 minutes remaining and winger Danny Galbraith for left-back Paul Hanlon as he desperately sought the winner.
Rankin stung the palms of Gallacher with a right-foot shot in the 74th minute and the visiting keeper had to tip away Kevin McBride's fierce drive four minutes later.
With 11 minutes remaining Benjelloun almost redirected Riordan's cutback into the net but instead saw the ball squirm just wide of the far post.
But St Mirren's brave resistance was finally broken with eight minutes remaining as the replacements combined.
Riordan played a short corner to Galbraith and Benjelloun headed in the winger's cross from six yards out before racing into the arms of his manager.
Gallacher clawed a Riordan shot away from his top corner and Benjelloun had a shot touched wide as Hibs finished with their tails up.
However, Billy Mehmet almost grabbed an equaliser with four minutes remaining, only for McBride to deflect the striker's shot over the crossbar.