Miranda, Raul Garcia and Filipe Luis all struck before half-time and a persistent Diego Costa rounded off the win late on, having previously missed from the penalty spot.
Diego Simeone's side now have an unassailable seven-point lead at the top of the group and will play in the knockout stages for the first time since 2008/09, while Vienna are still seeking their first win.
Atletico made just one change from the weekend win over Athletic Club, with David Villa dropping to the bench to be replaced by Raul Garcia.
Vienna named an unchanged side from the victory over Wiener Neustadt, although Alexander Grunwald, Alexander Gorgon and Marko Stankovic remained sidelined through injury.
The hosts won the corresponding fixture 3-0 in Vienna and took just over 11 minutes to break the deadlock this time around.
Vienna failed to clear a whipped corner from Koke, leaving Miranda to pounce and power home from close range.
The goal was arguably harsh on Vienna, who started the game brightly with Roman Kienast wasting a decent opportunity in the opening exchanges.
However, the visitors nearly fell further behind as Garcia dragged a shot just wide, before Costa weaved his way through the defence only to be denied by a magnificent save from Heinz Lindner.
Thibaut Courtois produced a great stop of his own at the other end, keeping out a well-struck effort from Daniel Royer in what proved a rare attack for the visitors.
Atletico continued to press and doubled their lead in the 25th minute when Garcia rose to meet Costa's teasing cross and expertly flicked a header past Lindner.
The 23-year old goalkeeper was tested again just over a minute later, tipping over a sweetly hit dipping volley from Costa.
Lindner still had to pick the ball out of the net again just before half-time, Filipe converting a simple finish after Juanfran’s scuffed shot had been palmed away.
Atletico began the second half in similarly dominant fashion, with Costa continuing to cause problems for the Vienna defence.
The Brazilian burst through several challenges before forcing Lindner into a smart save.
Vienna became noticeably frustrated at the back, giving away several free-kicks in dangerous positions as the game wore on.
They were almost made to pay just after the hour mark when an inviting ball from Koke was met by the head of Garcia, who was denied by Lindner from close range.
Costa continued his search for a goal, and was presented with a great opportunity 15 minutes from time when substitute Christian Rodriguez was brought down in the box.
The Brazilian's spot-kick was well saved by Lindner, but Costa was rewarded for his perseverance several minutes later when he found the net with a curling finish.
