A Lee Frecklington strike on 32 minutes levelled matters before top-scorer George Boyd fired Posh into the Third Round with a 64th minute blast that beat keeper Richard Wright at his near post.
"I felt the penalty save by the big man was the turning point," Fergie said after the 2-1 win.
"To go 2-0 down would have been difficult.
"We conceded another early goal which is driving me mad. I think the referee should start the game on 20 minutes.
"We needed to stop the rot but it doesn't mean anything unless we get a win next Monday night against Crystal Palace."