Ferguson left midfielder Michael Bostwick on the substitutes' bench and handed full debuts to forwards Conor Washington and Josh McQuoid as well as centre-back Jack Baldwin.
Defenders Nathaniel Knight-Percival and Ben Nugent missed out at Bramall Lane because of injury, but both could return for the home match with Crewe on Saturday.
The 2-0 loss in South Yorkshire means Peterborough remain sixth in the Sky Bet League One table - five points ahead of seventh-placed Swindon but 10 points behind Rotherham who are immediately above Posh.
"That was a poor performance," said Ferguson. "We played with no tempo in the first-half. We pride ourselves on our quick passing, but we were too slow moving the ball forward and it made it very easy for them to defend against us.
"I freshened things up as well with the intention of putting some zip in our play. I picked the right team for the game, but they just didn't deliver the performance.
"Britt (Assombalonga) did take a knock on Saturday at Crawley, but he's also feeling the effects of a long season physically. We know his form tailed off towards the end of last season and we don't want that to happen again.
"I want all our players to be fresh for the play-offs, but we missed a good chance to get eight points clear of seventh which is very disappointing.
"You have to credit the opposition sometimes. We knew exactly how they would set-up. We knew they would let us come on to them and then attack us on the break and they do it very well.
"I wasn't happy with our first-half performance, but at least we were level. The second-half couldn't have started any worse for us though as they scored with a great free-kick and from then on we just couldn't break them down despite plenty of possession."