Late goals from Ricardo Fuller and Bradley Pritchard piled the misery on the Posh and their 518 visiting fans at The Valley.
They remain rooted to the bottom of the Championship table having now taken just one point from a possible 18 available this month.
"The better team lost," said Ferguson. "It is just unfortunate maybe the way things are going at the moment.
"We didn't get a break, like the one that spun off Lee Tomlin and hit the post. We had a very, very, very good performance.
"I think you've got to take the positives out of any game and I've seen enough tonight to tell me we'll be okay.
"I think if any neutral had been at the game tonight and had looked at the league table before the game, that performance would not suggest we deserve to be at the bottom.
"I thought there was some really good performances and, as I said, the better team on the night lost the game but that is football."