Keen to put behind them the 6-1 thumping by Manchester City in the Premier League in their last match at Old Trafford, United burst out of the blocks with an eighth-minute Antonio Valencia goal but were lacklustre for most of the game.
After squandering several chances the English champions finally made sure of the three points in the Group C encounter when Rooney's 87th-minute strike was heavily deflected by Cristian Sarghi for an own goal.
There were raised eyebrows when a teamsheet featuring Rooney in the heart of midfield appeared but Sir Alex Ferguson's decision paid off as the England striker called the shots from deep.
"He was our best player," Ferguson told a news conference.
"He showed great awareness of that role, his selection of passes was very good, he showed great energy and determination, we got a really good performance out of him tonight.
"We have injuries and that's one of reasons we played him there," he added, referring to the likes of Tom Cleverley, Michael Carrick and Darren Fletcher.
"It was an option, a good option, he has all the qualities you need to be a central midfielder."
Ferguson had observed in his programme notes that what should have been an easy group on paper was proving much more competitive than expected.
But his side have hardly helped themselves.
Draws in their opening group games were followed by an unconvincing victory in Romania against Galati and they have now completed a double over the competition debutants with two far from sparkling performances.
Nevertheless, the three-times European champions find themselves top of the group, with eight points from four games, level on points with Benfica with two games to play. FC Basel are third with five and Galati are without a point.
"We've done a job tonight, we had to win and in the Champions League there are no easy games," Rooney told Sky Sports. "It's difficult. They worked hard and it was difficult to break them down."
The Old Trafford crowd, keen to erase memories of last month's derby defeat, must have been thinking of a rout after the early goal and seeing their team's attacking line-up.
United went in front when Dimitar Berbatov's pass found Phil Jones on the right and the defender's cross was tapped in by Valencia after it was missed by a charging Michael Owen.
That was the last action for Owen who limped off with a thigh injury three minutes later as the hosts were forced into an 11th-minute substitution, bringing on Javier Hernandez.
United could not muster a second goal in the first period despite chances for right back Jones, who spent most of his time attacking, Fabio and Anderson.
The Romanian champions laid their cards on the table when they named six defenders in their line-up and waited until just before the break to test United keeper David de Gea.
The Spaniard easily caught Ionut Neagu's speculat
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