Dons defender Gary MacKenzie capitalised on a rare mistake from Posh goalkeeper Joe Lewis to score the only goal of the game and make it five consecutive wins for the Dons, which ensured they leapfrogged Bournemouth into fifth place.
Dons midfielder Peter Leven was denied by the post, as was George Boyd for the visitors in an entertaining encounter at stadium:mk.
Ferguson said: "It's disappointing. It's a game I don't think we deserved to lose but we have, so well done to Milton Keynes for that.
"For once I'm standing here saying that we weren't ruthless, normally it's a side of our game that we're really spot-on with."
Ferguson added: "We get on with it, we go again. I thought the performance in general was good. I thought we were dominant after the first 10 minutes and I felt at half-time we would go on and win it."