The under-fire coach was pleased that the Rossoneri were able to salvage a point after his team fell behind in the first half of their Serie A fixture on Tuesday evening
Goals from Riccardo Montolivo and Stephan El Shaarawy cancelled out strikes from Fabrizio Miccolli and Franco Brienza as the away his side came back from two goals down to grab a 2-2 draw against Palermo in Sicily.
"It was a good comeback and we could have won," Allegri told a press conference.
"I really wasn't expecting to be 2-0 down after 47 minutes. We could have done better in the second half… The substitutes changed the game for us.
"El Shaarawy was not in great shape physically and I wanted to give [Urby] Emanuelson a rest as I can't burn them out, and that's why I decided to play with this system.
"The players are very good at understanding exactly what's asked of them. We can't play with the same players every three days, so that's why we needed to change the formation, to give them time to get their breath back."
Allegri also reserved praise for some of his 'quality' players, who have suffered from a tough spell of games, and conceded that given the circumstances, a point was not a bad result.
"With Montolivo, El Shaarawy, Bojan and Emanuelson, you can see on the pitch that they have quality. When you play every three days, changes are necessary," he added.
"I'm sorry for the players that they didn't win but a draw is acceptable tonight."