His resignation follows a dismal season for the Buccaneers who finished in 11th place.
In a statement issued on Wednesday, Jonevret thanked Orlando Pirates Football Club chairman Dr Irvin Khoza and supporters for giving him the opportunity to lead the team.
“I would like to thank the club for the opportunity,” he said. “Unfortunately it didn’t work out as planned. I wish the club and its supporters all the best for the future.”
Jonevret joined Pirates in February on a three-year contract, but has failed to stabilise the team and return it to its glory days.
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Instead, it was the first time the team failed to finish the season in the top eight since the PSL started in 1996.
Prior to his appointment, Pirates had been without a head coach for three months following the departure of Muhsin Ertugral in November last year.
Ertugral left after the team suffered a 6-0 loss against SuperSport United.
Khoza wished Jonevret well in his future endeavours.