City will face Barcelona in the last 16 on February 24 and March 18 but are forced to operate with a reduced squad of 21 after breaching UEFA’s Financial Fair Play rules.
And, having signed forward Wilfried Bony from Swansea when the transfer window was open, Pellegrini has decided to leave Montenegro international Jovetic out of his squad for European matches.
Jovetic told the Sunday Mirror: “I deserve to play in the Champions League, I know that.
“The manager has killed me with this decision. I feel I deserve my place and other people have told me the same. People have told me I am a great player but it is clear that the manager does not think the same way.
“I am very disappointed, even now. I don’t think it was a good decision or the right decision.
“I know that I deserve to be on the list. I told the manager this but he did not want to listen to me. I came here to play in the Champions League.”
The 25-year-old Jovetic joined City for £22m from Fiorentina ahead of the 2013-14 season but now fears his future may lie elsewhere, although he has vowed to work hard for the rest of the season.
“I have not made any decision about my future,” he said. “I will wait until the summer, then we will see.
“But the manager has put other players ahead of me, so maybe this is a message about what he wants to do.
“It is difficult to be focused when something like this happens but I am a professional and I want to show that I can still play a big part this season.
“This is a bad time for me but I am working hard and I will be there for the team. When we play Barcelona, I think it will be very difficult for me.
“This year, every time I have played, I think have done well. I don’t feel I have had a chance. OK, I have had injuries but so have other players.”