The young striker came off the bench to nod home a Paul Keegan free-kick in the 94th minute to seal a precious victory for the Gyspies as they kept pace with Cork City at the top of the table.
Last year's champions, who went into the game on the back of two defeats, looked like they were about to drop two more points as they were continuously thwarted by a resolute Drogheda back-line. However, Alan Matthews' side were dealt to crushing blows in the closing stages with Paul Crowley ordered off on 88 minutes for a bad challenge on Jason Byrne, before Hughes grabbed the winner for Bohs with virtually the last touch of the game.
It was a much changed Bohs side which started the game with Glen Crowe, Gary Deegan, Joseph Ndo and Owen Heary all missing through injury, while Jason McGuinness was suspended. Jason Byrne and captain for the night Glen Cronin were restored to the starting line-up following the midweek EA Sports Cup win over Wexford Youths alongside Brian Shelley and Conor Powell.
Matthews made just one change from the side which drew with Dundalk in their previous outing with Crowley coming into attack. Jamie Duffy had been due to start but when he was injured in the warm up Shane Barrett was drafted in.
Sixteen points and eight places separated these two sides before the game, therefore it was little surprise that Bohs started strongest, with Anthony Murphy proving menacing down the right. He played in Byrne with a dinked cross from the touchline in the opening minutes, but his close range shot was blocked by Alan McNally. Murphy then failed to trouble Steve Williams with a shot from 25 yards.
Byrne then really should have given the home side the lead on 12 minutes. Neale Fenn played a long searching ball over the top, which Byrne brought down superbly before dragging a shot wide from 18 yards.
Having spent the opening quarter camped inside their own half, Drogheda gradually began to force their way into the game and Shane Barrett almost put the Louthmen in front on 21 minutes. Barrett found himself unmarked at the back post but his thunderous volley from the tightest of angles was superbly parried around the post by Brian Murphy.
Buoyed by that close call, Drogheda continued to push forward and Conor Kenna passed up another decent chance for the away side just before the half hour mark, hacking a shot wide from eight yards.
The home side resumed control soon after, but again they failed to create anything of note in the final third. The closest they came was through Paul Keegan, whose goalbound effort from 25 yards was bravely blocked by Robbie Martin, before a Mark Rossiter cross narrowly evaded the head of the unmarked Byrne.
Bohs manager Pat Fenlon was clearly unimpressed by what he'd witnessed and introduced Killian Brennan at the interval in place of Graham Carey, who had been largely anonymous on the left wing during the first half.
Brennan almost made an immediate impact, dropping off inside the area to meet Keegan's deep cross, but the winger's shot was blocked by the outrushing Ian Ryan.
Whatever Fenlon said to his charges at half-time had clearly worked as Bohs continued to flood forward. Anto Murphy marauded down the right before cutting the ball back to Byrne, but the striker was a tad casual and saw his flicked shot from six-yards cannon clear off the legs of Williams.
The expected Bohs onslaught slowly began to materialise after the hour mark and Fenn looked to have put the Gyspies in front on 67 minutes when headed a Keegan corner goalwards. Williams caught the ball on the line and appeared to have carried it over, but the linseman didn't flag. Byrne also went agonisingly close just 60 seconds later when he latched on to Rossiter's through ball before unleashing a thunderous half-volley which blazed narrowly over the postage stamp corner.
With Cork City winning, Bohs knew they needed all three points to keep in touch at the top, but despite huffing and puffing it looked like Drogs were about to escape with a precious point. However their chances of holding on were dealt a major blow on 88 minutes when Crowley was shown a straight red card for a crude lunge on Byrne midway inside the Drogheda half.
Their numerical disadvantage was to be their undoing when young Hughes, introduced as a substitute for Fenn on 78 minutes, was left unmarked inside the six yard box where he nodded home a Keegan free kick for his first senior League goal and with it turned one point into three for the Gyspies. It was a cruel blow for Drogheda, who had defended resolutely throughout.
Extratime.ie man of the match: For 93 minutes Alan McNally was a rock at the heart of the Drogheda defence. However, he and his team mates fell asleep in the dying seconds allowing Mark Hughes to snatch all three points for Bohs. For being in the right place at the right time, Hughes takes the honours.
Bohemians: Brian Murphy, Mark Rossiter (Ryan McEvoy, 81), Conor Powell, Glen Cronin, Brian Shelley, Ken Oman, Anthony Murphy, Paul Keegan, Neale Fenn (Mark Hughes, 78), Jason Byrne, Graham Carey (Killian Brennan, HT)
Subs not used: Sean Byrne, Matt Gregg
Drogheda United: Steve Williams, Ian Ryan, Robbie Clarke, Conor Kenna, Alan McNally, Paul Shiels (Brian King, 68), Gavin Whelan, James Chambers, Shane Barrett, Robbie Martin (David O'Connor, 92), Paul Crowley
Subs not used: Paul Skinner, Mark Salmon, Eoghan Osbourne
Referee: D Tomney