The Montenegro striker was dropped from City's squad for the latter stages of Europe's premier club competition on Thursday, with January signing Wilfried Bony taking his place.
Jovetic's City career has never really taken off following his move from Fiorentina in July 2013, but Pellegrini says the 25-year-old can still have a future with the Premier League champions.
He said: "I don't think that one thing is linked with the other,
"It's very important for Stevan to try to play now until the end of the season. To try and play as much games as he can, try not to be injured and have a high performance every time he plays.
"At the end of the season we analyse, not just with Stevan, but also with the rest of the squad which will continue next year."
The City boss added: "It's always difficult to take a player out of the list, but we have restrictions this year [for breaching Financial Fair Play regulations].
"We bought Bony because we need another striker - a box player. And in the position of Jovetic maybe we have lots of other options.
"It's a difficult decision, but I think it's the best for the squad."
Jovetic started only one of City's six Champions League games so far this season and has made only 14 Premier League appearances - nine of those as a substitute.
