The Chilean tactician is, however, confident that City can cope should their top marksman be forced back onto the treatment table.
Aguero, who netted his 26th goal of the season and his 50th in Premier League competition for the Blues, limped off at White Hart Lane shortly before half-time.
It remains to be seen how long a hamstring complaint will sideline the Argentine striker for and Pellegrini is reluctant to speculate until he has all of the facts.
He said: "We will see tomorrow (Thursday) with the doctor.
"He has an injured hamstring so we will have to see how serious it is. We won't have any indications until tomorrow.
"Sergio is a top player but we don't depend on just one player so we hope it's the moment where Stevan Jovetic can play and hope that Sergio can join us again as soon as possible."
City's cause in north London was unquestionably aided by the dismissal of Tottenham full-back Danny Rose early in the second half, for a clumsy challenge from behind on Edin Dzeko.
Pellegrini, though, refuses to buy into the belief that Andre Marriner's decision to reach for his pocket changed the game, with it his opinion that the visitors were already well on top.
He added: "I don't think it was a big decision because before the red card we missed at least five clear chances to score in the first half.
"If we review the first 45 minutes I don't remember just one chance for Tottenham, I think our team was the best team from the beginning.
"If you ask me it was a clear penalty and a clear red card because he was the last man. The sending-off was not the thing that changed the game, the game was over and completed from the beginning for our team."