The player had lodged a case with the Premier Soccer League’s Dispute Resolution Chamber (DRC) in a bid to get his clearance from the club after claiming his contract has expired with the club.
However, the Chilli Boys have maintained that the former Orlando Pirates player still has two years left on his contract with the club.
According to a source, the DRC decision means Molongoane has now been forced to report back to Chippa United despite having already signed a pre-contract with Kaizer Chiefs.
"The case was heard this morning and unfortunately he [Molangoane] lost it," said the source. "He is now forced to go back to Chippa United."
Meanwhile, Chippa United boss Chippa Mpengesi said the doors are still open for Molangoane to return to the club.
"It's unfortunate that this matter has to go this route instead of being resolved without going to the DRC. The supporters of Chippa United love Joseph Molangoane and he's never been chased away from the club," said Mpengesi.
"Our doors are still open for him. If he wants to go we won't stand in his way. If any team is interested in signing him we are still available to talk."