Oldham enjoyed the best of the opening exchanges, with Neal Trotman missing two golden chances to open the scoring after a quarter-of-an-hour. But he atoned for his profligacy in the 32nd minute.
The defender met Mark Allott's cross at the near post and his stunning backward header found Hughes, who fired the visitors in front.
Millwall's passing was wayward at best in the first half. However, captain Paul Robinson found the key on 38 minutes, with a precision long ball from the back.
Winger Jay Simpson charged on to it, leaving the Oldham defence for dead, before blasting his shot across veteran shot-stopper Mark Crossley.
The midfielder raced over to celebrate feverishly with the New Den faithful.
But the smile was wiped off his face, when referee Kevin Friend gave him a second booking and sent him down the tunnel.
It was Simpson's second booking inside a minute after his foul on Oldham's Chris Taylor and the Lions faithful were fuming.
Being down to ten men did not halt Millwall's forward momentum, though, and Zak Whitbread charged in to head home Dave Brammer's free-kick on the stroke of half-time.
Neither side could find the breakthrough early in the second period. But Oldham took full advantage when Millwall's Bryan Hodge held Taylor back in the box.
Friend pointed to the spot and Hughes defied a crescendo of boos to put his spot-kick high past Lions keeper Lenny Pidgeley.
The former West Brom forward then sealed the points when he volleyed in a superb Allott long throw in the 80th minute.
Neal Eardley received a second booking for his part in the jubilant Oldham celebrations.
Hughes was then brought off amid a hail of missiles and boos from the home fans. But the visitors hung on to take the three points back to the north-west.