Jovetic, who will undergo a medical with the Serie A giants on Tuesday, represented City in just 28 Premier League games over two seasons, scoring just two goals.
While this is not the return that City would have hoped for from a player they paid Fiorentina £22 million for, Pellegrini has revealed that it is Jovetic's injuries rather than his lack of goals that resulted in his exit.
"Unfortunately, Stevan had to go," Pellegrini told City's official website. "He's a very good player – one of the best players I have seen – but for him he had too many injuries and that's why he couldn't play too many games in a row.
"I wish him the best for the future and I'm sure he'll be a very important player for Inter."
It is believed that the Montenegro international will initially join Inter on loan. There are conflicting reports as to the exact details of the loan, with one suggestion that it will be a two-year loan, and another that Inter will pay £2 million to take Jovetic on a season-long loan, after which they will purchase the striker for a fee of £10.25m which could rise to £12.25m.