"We arrived at a consensus after a lot of thought and in the best interest of the club a collective call was made," said the Pune club's President, Shirish Kulkarni, in a media release.
"I am extremely proud of my time and achievements at DSK Shivajians. I would like to thank the players, staff, the management for their efforts and support," said the 54-year-old Goa-born Pereira.
"I would also want to thank the most important and fundamental part of this club, the fans. Special thanks to Mr Shirish Kulkarni for giving me this opportunity at DSK Shivajians in what I believe has the country's best infrastructures for the sport," he added.
In the I-League, he guided the club to some memorable wins over Mumbai FC and Kingfisher East Bengal as well as leading the team to a commanding 3-1 win over Sporting Club de Goa, which turned out to be the biggest margin of victory for the club.
DSK Shivajians were placed ninth and last in its debut season with 15 points.