The Andalusian club has announced that the Chilean will leave La Rosaleda at the end of the season, ensuring that his jump into the Manchester City hot seat is imminent
The Chilean has been linked with a switch to the Etihad Stadium since earlier in 2013 and Roberto Mancini's sacking earlier in May added fuel to the fire that Pellegrini would be leaving La Rosaleda for the Blues in the summer.
The coach told his outgoing club's website that "sporting reasons" are behind his departure from the Liga side but believes the Andalusians have a good future ahead of them regardless of the split between coach and squad.
"Everyone has the right to follow their own path and Malaga have to take another now," he said. "The club have the funding and the will to have a successful future.
"I would like to thank the owners of the club for putting their trust in me. The most important foundation of this club is on the team and not individuals."
Pellegrini's Spanish side was seconds away from a place in the last four of the Champions League, before two late goals in the second leg quarterfinal against Borussia Dortmund knocked it out dramatically.
Despite its financial woes in the past 12 months, Malaga is in sixth place with La Liga almost at an end, and the former Villarreal boss will take charge of the team's final two matches before likely becoming a Premier League manager in June.
The coach, who spent a season in charge of Real Madrid before Jose Mourinho's arrival, is set to take over a Man City side which finished second behind Manchester United this season and lost in the FA Cup final to Wigan.