The Os progressed to the Wembley final 3-2 on aggregate after two tight affairs, with Posh facing another season in League 1 after losing at Brisbane Road.
They had their chances but fluffed their lines in front of goal, not least when Danny Swanson opted to shoot from the angle rather than cross for 33-goal Britt Assombalonga to tap in.
"The difference on the night was they were more clinical," Ferguson said.
"To have four three-on-three situations in the first 45 minutes and not take advantage of any of them, that was our downfall.
"In my opinion I don't know if Orient have done enough over the two legs to go through, but they have done.
"So I have to congratulate Orient and I really hope they go on and win it now."