Centre-back Joao Miranda got the ball rolling by scoring the first after 11 minutes, and soon Raul Garcia doubled the advantage with a headed goal.
Filipe Luis increased the lead on the stroke of half-time and then Diego Costa finally added his name to the scoresheet on 82 minutes.
Diego Simeone's side will go into the second round draw seeded as group winners, having won all of their four games, a record only matched by last year's winners Bayern Munich.
Los Rojiblancos, who had won all three of their previous group games, rested Spain international David Villa but otherwise fielded a full-strength team.
However, they were sluggish at the start, and it was the visitors who created the first opening, midfielder Florian Mader shooting narrowly wide of Thibaut Courtois' left hand post with just five minutes played.
The hosts quickly burst back into life after conceding the chance and began attacking.
It did not take long for their guests to cave in.
Koke swung in a corner into the six-yard box which was not cleared, and Miranda was quickest to the loose ball, taking one touch before bundling it over the line.
Atleti were not satisfied with the one goal and immediately sought another.
Garcia shot just wide of the near post from the edge of the area, and then Costa had a better chance, racing into the box with options to pass, but went alone and in the end took too long to shoot, allowing Austria Wien goalkeeper Heinz Lindner to keep it out.
The visitors should then have made Atletico pay.
Thomas Murg received the ball alone in the box with his back to goal and turned quickly but Courtois raced off his line to make himself big and thwarted the winger.
Four minutes later, Atletico got back in control by finding the second goal.
Costa got down the right wing and beat a defender before curing a fine cross towards Garcia, who leapt up to send a header looping over the hand of the outstretched Lindner and into the back of the net.
Costa nearly made it three a few moments later, finding himself with just Lindner to beat, but the shot was complicated by the angle, and this time the goalkeeper was able to parry.
But the third goal would arrive soon enough.
Just as half-time was approaching, Koke switched the play from the left to find Juanfran on the right. The full-back dragged the ball into the box for Adrian, who got little power on his shot, but Lindner could only palm the ball back into the danger zone and Luis was waiting to knock the ball in from just two yards out.
The sizeable advantage allowed Simeone to give second half appearances to Cristian Rodriguez, 18-year-old prodigy Oliver Torres and French midfielder Josuha Guilavogui, who had only previously played one minute of competitive football for the club he joined in the summer.
Atletico somewhat took their foot off the pedal in the second half, but Wien posed no further threat.
Costa was determined to get on the scoresheet but had to strive for the privilege.
First he failed to get on the end of a cross from Luis, then he was denied twice by Lindner.
His frustration looked to be about to end when Atletico were awarded a penalty after Manuel Ortlechner fouled Rodriguez.
However, the Brazilian-born striker, who is set to represent Spain at next summer's World Cup, saw his effort saved by Lindner.
But the joint-top scorer in Spain's Primera Division would not be denied the goal his omnipresent performance warranted, and with eight minutes remaining received a backheeled pass from Raul Garcia just outside the area, and smacked it into the net, finally getting the better of Lindner.