The Manchester City manager says the forward has a place, despite his Champions League omission.
The Chilean manager was forced to omit the Montenegrin forward from his European squad on Thursday, replacing him with January signing Wilfried Bony.
The decision to leave out Jovetic was an enforced one as a result of the club being punished for failing to comply with Financial Fair Play, and being forced to name reduced squad in this year’s competition.
Pellegrini admitted that leaving the striker out of the squad was not entirely straightforward, but he believes the decision was the right one for the squad further down the line.
"It's always difficult to take a player out of the list," he said.
“But we have restrictions this year. 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."
The omission from City’s squad has led to suggestions that Jovetic now has no future at the Etihad, and he was linked with a return to Italy by the Express during the January transfer window.
However, Pellegrini has rejected those suggestions that he will leave the club in the future and insisted that he still has an opportunity to succeed at the Premier League champions, although he didn’t rule out an exit entirely.
“I don't think that one thing is linked with the other," he added.
"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."