A minute before half-time Rooney was felled by Dons keeper Jamie Langfield inside the box, allowing the former Tottenham midfielder to slot home his first spot-kick since the Champions League final penalty shoot-out win over Chelsea in Moscow.
Rooney headed home number two from Darren Fletcher's cross in the 69th minute before going off to a standing ovation minutes later.
Ferguson was pleased with the run-out and especially the contribution of Rooney.
He said: "It was a good day for me, it was emotional driving up to the stadium and seeing people you haven't seen for years.
"It was our first game and it was quite an open match and easy for both teams.
"They had a couple of chances and we had to defend well at times so it was good.
"Wayne had a couple of chances in the first half and made some nice runs round the shoulders of defenders which could have got us a couple of goals.
"He made the goal and scored the header so he will be happy."