The Serie A side eased the pressure on manager Vincenzo Montella with a repeat of the 5-1 triumph in the reverse fixture back in September.
Andre Silva scored a hat-trick on that occasion and the striker netted two more on home turf, while fellow striker Patrick Cutrone also found the net twice in a comfortable victory.
Ricardo Rodriguez scored the home side's first of the night after Wien had taken a shock lead, Christoph Monschein breaching Milan's flimsy offside trap to break the deadlock midway through the opening half.
However, with the legendary Kaka watching on from the stands, Milan ended a four-game goal drought in front of its own fans in emphatic fashion, in the process securing top spot in Group D.
Having lost 2-1 to Napoli at the weekend, Montella's side – which had led 3-0 inside 20 minutes in the first meeting – started sluggishly before the shock of conceding lifted them out of their early slumber.
Wien stunned its host in the 21st minute, Monschein breaking through to round goalkeeper Gianluigi Donnarumma and score from a tight angle. Despite Leonardo Bonucci's desperate slide, the ball deflected off the centre-back's heel before trickling over the line.
The advantage, however, lasted just six minutes. An unmarked Rodriguez converted Fabio Borini's right-wing cross at the back post to bring Milan level.
The Swiss defender was also involved in his side's second, as his weak free-kick rolled perfectly into the path of Andre Silva, who capitalised on the unexpected opportunity by slamming home a low shot.
Cutrone joined his strike-partner on the scoresheet before half time too, nodding in Borini's cut-back cross as goalkeeper Patrick Pentz was caught horribly out of position.
Bonucci failed to provide the final touch in the right net shortly after the interval, volleying over from a corner, before Silva put the game out of Wien's reach with his second of the night in the 70th minute.
The Portugal international took his tally in the group stages to six in five matches, though his weak shot on the turn only made it to the net due to Pentz's right foot getting stuck in the turf as he attempted to make a save.
Pentz did prevent Silva from securing another European treble against Wien, turning aside a stinging drive, but Cutrone added a fifth in injury time, the teenager waltzing around the beleaguered goalkeeper to complete his double and repeat the result from Vienna.