The Belgian tactician joined Rise and Shine at the start of the season and helped them to end the first half of the campaign in sixth position in the league, the first time the club has reached that high.
Eymael has been unhappy at how things have been going behind the scenes and appears to have fallen out with chairman Jonny Mogaladi.
“I just want to inform that I have given my resignation to the club at 1pm,” Eymael tells KickOff.com.
“It is for private reasons and because I couldn’t agree on different things that happened in the last couple of weeks.”
The former AS Vita Club coach leaves the club lying seventh on the log with 26 points from 20 league matches. The 57-year-old was in charge of 22 matches in all competitions, winning six, drawing 11 and losing five.
His last game was Wednesday night’s 3-1 victory over African All Stars in the Nedbank Cup round of 32 at Peter Mokaba Stadium, which ended a seven-game winless streak.