Ferguson watched Posh let an early lead slip at the Madejski Stadium as goals from Simon Church, Adam Le Fondre and Hal Robson-Kanu rendered Tommy Rowe and Emile Sinclair's efforts redundant, ending the visitors' three-match unbeaten run in the npower Championship in the process.
The Peterborough boss insisted his team had been in the ascendancy for much of the contest, and stressed that he was pleased with the overall performance of his players despite the defeat.
"(It is a) really disappointing result. I'd have been disappointed with a draw the way the game went. I thought we deserved more, especially after the first half," Ferguson said. "We outnumbered them and passed the ball well and I just wanted the second goal which we didn't get.
"We shouldn't be talking about a defeat but we are. You can't blame the defence, the first two goals came from a striker defending - which they're not very good at.
"I was pleased with the performance. We needed to get back a bit of fluency in our game, which is what we've been missing in our last two games - it's been a bit of a grind. We got that but Reading are a good team and they've got some good players and a very good manager. We functioned well as a team but we've lost three goals."