United failed to make it out of their group in 2011-12, but on Wednesday sealed top spot and a place in the knockout phase after only four matches as they came from behind to beat Braga 3-1 at the Estadio AXA, maintaining their 100% record.
Now with 12 points, United can go into their final two group fixtures knowing they cannot be caught by Cluj or Galatasaray, both on four points, or Braga, who have three.
Reflecting on United's surge into the next round, Phelan said: "Our intention this year was to get into [the knockout phase] very quickly.
"We were disappointing last year - the players and staff knew that, and I think the supporters wanted a reaction to that.
"I think it was really important that we got into it quickly and we have done that - four games gone and we are more than happy with it."
As they have on several occasions this season - including two of their previous three Group H games - United conceded the opening goal, which came four minutes into the second half.
Custodio collided with Jonny Evans in the box and Alan, scorer of Braga's two goals when they went 2-0 up at Old Trafford last month before eventually being beaten 3-2, smashed home the resulting penalty.
A United side showing six changes from Saturday's Barclays Premier League win over Arsenal had struggled to get into the contest up to that point and not long after Alan's goal, a power cut which saw some of the floodlights go out led to a break in play.
The visitors emerged for the resumption around 15 minutes later with Rio Ferdinand on for Evans, and after Robin Van Persie and Rafael also entered the fray for Danny Welbeck and Nani, the tide turned.
Van Persie expertly guided the ball from outside the box over stranded goalkeeper Beto to equalise, before a penalty from Wayne Rooney - who had missed one against Arsenal - and a late Javier Hernandez effort wrapped up United's win.
Phelan admitted the way things had turned out had been surprising and suggested the power cut hold-up had been to United's advantage.
"It is a little bit surprising that we have scored three goals here tonight [Wednesday]," Phelan said.
"In the first half we were not really doing anything in the game other than keeping possession of the ball.
"Possibly with the way the evening panned out - with the lights going out and the heavy rain, and then us having to make a quick substitution, bringing Rio Ferdinand on - that changed things for us, with the tempo of our game going up.
"Robin was instrumental in getting us further up the field. We played a little bit more in behind their midfield once Robin came on, and obviously he took his goal really well.
"It fell to him in a very good position on his left foot, he saw the goalkeeper probably trying to get to the ball a bit too quickly, and managed to hit it into the back of the net."
On Rooney's penalty he added: "We were actually surprised that he took it. We thought maybe someone else would step up to take the penalty, but credit to him - he wanted to get that disappointment behind him quickly and he finished it."
Asked if any United players had picked up injuries, Phelan said: "Jonny Evans felt his groin a little bit - I think it probably happened during the penalty incident.
"He did start feeling his groin, so as a precaution we took him off quickly.
"With Nani I think it was probably just a lack of games and his hamstring started to tighten up, so we weren't taking any chances with that."
Van Persie netted in the 80th minute, Rooney five minutes later and Hernandez in stoppage time to leave Braga stunned.
The Portuguese side's coach Jose Peseiro felt the final scoreline had been harsh on his team and praised them for their efforts.
"I didn't see a clear opportunity for Manchester United until 80 minutes," Peseiro said.
"I think they played well after the lights went off and we made some mistakes, which will happen against Manchester United.
"But in this game I think my team was fantastic - better than at Old Trafford. My team did not deserve this result, in my opinion."