Daniel Powell was given a rare start by Dons boss Karl Robinson after striker Aaron Wilbraham joined Norwich on Friday and he opened the scoring with a 20-yard bullet.
Peter Leven finished Rovers off three minutes later with a low free-kick and Patterson admitted his side were lucky to only be 2-0 down at half-time.
He said: "We looked like we hadn't played for longer than three weeks. When we got the ball we gave it away quickly and then we were chasing shadows - it was a vicious circle for the first 20 minutes.
"I was very pleased to get in at 2-0 down at half-time. I changed it second half and I thought the substitutions worked very well - we were much better, a lot more attack-minded and passed the ball better."
Rovers face Plymouth next up and Patterson is seeking a response from his players but stopped short of saying whether he would like to land the role permanently.
He added: "I'm kind of hoping that's the rustiness out of the way and we can kick on and get some valuable points on the board on Tuesday. That is a million miles down the road right at this moment [about whether he wants the job on a full-time basis] so I'd rather not answer."