The Chilean saw his side create very little in the way of chances, and had goalkeeper Joe Hart and some wasteful finishing from the Potters to thank for a share of the spoils.
City fielded six changes from the side that beat Hull City before as Pellegrini prepares for a Champions League tie against Viktoria Plzen on Tuesday, but he insists those changes were not the reason for an underwhelming display.
"Disappointed with the performance? No," he told reporters. "But I agree that we didn’t have many chances to score, but when you play away and cannot win you must at least not lose and I think that’s important for us.
"I have trust in the squad, I don't think that we didn’t play well because we made changes. Stoke also had a very good match and that's why we couldn't have a clear chance to score.
"I don’t think you must expect us to win every match, of course we want to but it's impossible to do it.
"I will not always be happy to draw away but for this match it is a good draw."
Pellegrini was particularly pleased with the performance of Hart, with the goalkeeper making smart saves from Kenwyne Jones and Charlie Adam to record his fourth consecutive clean sheet for club and country.
"I always trust in Joe Hart," the City boss added. "I have never had doubts about him.
"For him it's very important to have a clean sheet again. The last four games, that’s always important for a goalkeeper and I'm sure Joe will continue doing the work we know he can do."
There was also positive news for City on the fitness of captain Vincent Kompany - the Belgium international limped out of their opening-day win over Newcastle with a groin injury, but Pellegrini expects him to be fit for the Manchester derby in a week's time.
"We'll see tomorrow and Monday if Vincent can play next Tuesday in the Champions League," he explained. "But sure he will arrive to the derby."