The Chilean has been linked with a move to Premier League Manchester City who are looking for a manager after sacking Roberto Mancini.
"Professionally, these are my final hours at Malaga," Pellegrini said at an awards ceremony in the Costa del Sol city, according to local media.
"On Sunday, I will take charge of my last match at the Rosaleda. Everyone has the right to follow their own path. I am not leaving because of financial ambition, but because of a sporting project that will allow me to feel fulfilled."
He gave no further details about his future.
Malaga are sixth in La Liga and host Deportivo La Coruna on Sunday as they chase a place in the Europa League next season, though they would not be able to take it up unless a UEFA ban, imposed because of delays in payments to creditors, is overturned.
Their final game of the season is at Barcelona on June 1.
"It's going to be very emotional and we hope to leave the club with a place in European competition," the 59-year-old Pellegrini added.
"The agreement with the club has been gratifying and satisfactory."
The former Villarreal boss, who joined Malaga after being sacked by Real Madrid in 2010, led the Qatar-owned club to the Champions League quarter-finals in their debut season, where they lost to finalists Borussia Dortmund.
Known as 'The Engineer', Pellegrini has had a strained relationship with the club and its owners over their long-term commitment to the project.
After an initial investment in playing staff when they took over in 2010, the owners have sold some of their best assets including Santi Cazorla and Nacho Monreal to Arsenal, and Salomon Rondon to Rubin Kazan.
Malaga have appealed against the UEFA one-year European ban to the Court of Arbitration for Sport (CAS) and expect to get a ruling early next month.