Rooney has a mixed record with spot-kicks and became the fourth United player to miss one this season when he struck wide in United's 2-1 Premier League victory over the Gunners at Old Trafford on Saturday.
But that did not deter him from stepping up four days later to take on the responsibility again when the Red Devils were awarded another one with five minutes of normal time remaining in their Champions League Group H clash at the Estadio AXA.
After substitute Robin van Persie's 80th-minute effort had cancelled out Alan's opener - also a penalty - for the hosts four minutes into the second half, it was an opportunity to put United in front for the first time and Rooney, who had earned the spot-kick when Nuno Coelho was adjudged to have fouled him, made the most of it by beating goalkeeper Beto with a firm shot.
The 27-year-old appeared to skid a little on the wet surface as he fired the ball in and he conceded afterwards that he had been "a bit fortunate".
Asked if he had had any doubts about taking the penalty, Rooney said: "No, not at all.
"Obviously I was disappointed at the weekend, not only to miss but to miss the target.
"I said after the game it wasn't good enough and (against Braga) I was a bit fortunate; I slipped but thankfully it's gone in so I'm happy with that.
"At the time it happened so quick, but obviously I've seen it going towards the goal and the keeper going the other way.
"I was happy with it going in but obviously I've been quite lucky with that."
With Javier Hernandez adding a close-range finish in stoppage-time, United went on to complete a 3-1 victory that was their fourth win in four Group H fixtures and guarantees them top spot and a place in the last 16.
It was the just the latest in a host of come-from-behind wins for United this season that had certainly not looked on the cards for most of the contest in Portugal, which they had struggled to really get going in and was halted for around 15 minutes not long after Alan's goal by some of the floodlights going out in a power cut - seemingly to the visitors' benefit.
"I think we can play better football - at times it was too slow but the result is the most important thing," Rooney said.
"I think we had quite a bit of possession, we just needed a bit more movement and speed to our play, and thankfully in the last 10 or 15 minutes, when it mattered, we got them."
Veteran United midfielder Ryan Giggs, who came into the first XI as one of six changes from the Arsenal game, felt the introduction of Van Persie shortly after the resumption of play following the power cut was crucial.
The striker subsequently netted his 11th goal of the season by expertly guiding the ball over the stranded Beto from outside the box when the goalkeeper rushed out too soon, and Giggs can see why some of his team-mates have been drawing comparisons between Van Persie and his fellow Dutchman, the former United frontman Ruud van Nistelrooy.
"It wasn't until after we went 1-0 down - probably when Robin came on - that we started to play a little bit better," Giggs, 38, said.
"His confidence is just sky high at the moment.
"I read last week that a lot of the players think he's similar to Ruud in the respect that Ruud used to get a chance and more often than not he'd put them away.
"That's the case with Robin at the minute; his confidence is high, we're creating chances for him and he's putting them away."
With a maximum 12 points, United - who also currently lead the Premier League - are eight points clear of Galatasaray and Cluj in Group H, and nine in front of Braga, with two rounds of group games to go.