Rooney, making his first start for United since October and the fall-out from his contract negotiations, netted his second goal of the season to ensure Sir Alex FergusonÃ¢â‚¬â„¢s men maintained their unbeaten record which now stretches to 27 games.
The striker sent Rangers goalkeeper Alan McGregor the wrong way after Stephen Naismith conceded the penalty for a high footed challenge on United full-back Fabio.
With his team only needing a point to secure qualification to the next stage, Ferguson took the opportunity to rotate his side by giving starts to Jonny Evans, Chris Smalling, Fabio and Ryan Giggs.
Despite having the majority of possession in the first half United struggled to get past the home sideÃ¢â‚¬â„¢s rigid defence, with Rooney coming closest when he hit the bar with a header after good play from Fabio down the left-hand side.
The Scottish champions were happy to sit back and hit United on the counter, and could have taken the lead before half-time had Kenny Miller squared the ball back for Vladimir Weiss instead of shooting from a tight angle.
The second half was a much more open affair with both teams searching for the win. Michael Carrick produced a good save from McGregor in the 54th minute after some good interplay between Rooney and Dimitar Berbatov on the edge of the box.
A few minutes later a mix up in the United defence between Evans and Van der Sar allowed Naismith in, but striker was denied by a good save from the veteran United shot-stopper.
It seemed as if it was not going to be United or RooneyÃ¢â‚¬â„¢s night after the striker missed two chances in as many minutes. First his diving header went wide of the near post in the 73rd minute, and then he failed to connect with ball on the volley after Berbatov played him in with a delightful chip.
Rooney was not to be denied however and the strikerÃ¢â‚¬â„¢s jubilation was evident after he finished clinically from 12 yards.
United now only need a point from their last game against Valencia at Old Trafford to guarantee themselves the top spot in Group C.
Ferguson later admitted Rooney is still lacking match fitness but praised his striker for stepping up to take the spot-kick. “It took a lot of courage to take the penalty,” said Ferguson.
“It was not an easy night, he missed a couple of chances but that’s what you expect with the rustiness in his game. We are pleased for him.”
He added: “Every time he scores a goal he wants to celebrate with the fans and players.”
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