The Chilean coach refused to let his stuttering side's form on the road worry him despite a run of only three victories from their last 11 away league games dating back to last season.
"It's important to keep calm. In general I was very happy with the way my team played today and we deserved a different score," he said. "We played very well and deserved to win."
They started well against Villa and dominated the first half but missed lots of chances before Yaya Toure opened the scoring with his fourth goal in their six league games this season.
Pellegrini's side would come to rue their profligacy in front of goal as they twice squandered the lead.
Villa's Karim El Ahmadi equalised early in the second half before Edin Dzeko restored City's lead. The hosts then scored twice in three minutes to turn the game on its head with Leandro Bacuna's magnificent free-kick and Andreas Weimann's winner.
"We played very well and deserved to win," a frustrated Pellegrini told Sky Sports. "We deserved another score in the match, but in five minutes we did two things that threw away everything good we had done in the rest of the match.
"The way we lost this game was incredible. We led twice, and we had control of the game."
Villa manager Paul Lambert praised the way his side overcame a crippling injury list to claim a third league win of the season that takes them up to ninth place with nine points.
"I thought we were outstanding. The injury list is pretty horrendous. We've lost two lads (forwards Christian Benteke and Gabriel Agbonlahor) who have scored a lot of goals for us and we've lost (Ashley) Westwood who has been fantastic.
"We're up against one of the best teams in the country. Not just for the Barclays Premier League but for Champions League football so that says a lot about the magnitude of the result.
"I know from experience reputation will never win you the game. Their two lads (Toure and Brazilian Fernandinho) played well but El Ahmadi, (Yacouba Sylla) and (Fabian) Delph were absolutely brilliant."