Argentina striker Aguero was without a goal in five appearances across all competitions since his return from a knee ligament injury sustained in December.
City were winless during the same period, allowing Chelsea to open up a seven-point advantage at the Premier League summit.
But Aguero opened the scoring with a wonderful solo effort at the Britannia Stadium and converted a second-half penalty to move his tally for the season to 21 after being booked for netting with a handball on the stroke of half-time.
An eventful evening for Manchester City's talisman concluded with him limping out of the action, but Pellegrini allayed fears that his knock to the back was a serious problem.
"He felt something in his back but my feeling is that it is not too serious," the Chilean told his post-match press conference, before pointing out that Aguero is one of a handful of City players working their way back to full fitness following a heavy bout of injury problems before Christmas.
"When Sergio has more minutes he will return to his normal performance.
"He scored one goal, he scored the penalty - I think it is important for him, Samir Nasri, Vincent Kompany, Edin Dzeko and all the players who have had long injuries to have more minutes because they will improve.
"It's very important for Kun to be fit. If he plays for three months in a row you will see how good he is.
"This year he had that problem in his knee. He didn't have any muscle problems and that is important for him.
"We hope if he continues playing every game from now until the end of the season we will see what we know he can do."
Peter Crouch scored a deserved equaliser for Stoke before the defending champions turned in a dominant second-half display.
James Milner and Nasri were on target either side of Aguero's penalty, although a last-gasp strike by Willian saw Chelsea beat Everton 1-0 to preserve their lead.
Nevertheless, Pellegrini insisted that did not take the shine off an evening when he was firmly focused on his own team emerging from their recent slump.
"We are not thinking about Chelsea," he added. "Obviously if they lose points it is good for, us but the first thing for us was to recover the sensation of a good team, a solid team.
"That was the target and we did it."
