The former Rise and Shine assistant coach took the head coach post at the start of the current Betway Premiership season.
He replaced Phuti Mohafe, who left Rise and Shine to join Marumo Gallants, where he only lasted a few months before his departure.
Now Moloto has parted ways with the struggling club, that finds themselves in 11th place on the league standings with just eight points from their opening nine games.
He told Soccer Laduma: “Yes, I have resigned. I have decided to put the team first.”
Despite joining the club in July, he has not been with the team for the past two months after suffering with ill health.
Moloto is said to have fallen ill during the league clash with AmaZulu at the Peter Mokaba Stadium in September. He was taken to hospital after reportedly collapsing at the venue.
READ: Carling Knockout: Siwelele FC advance after dramatic penalty shoot-out victory over Polokwane City
He had been recovering slowly and made a brief return to the club before being booked off again and has now decided to call time on his Polokwane tenure.
“I’ve been away from the team for almost two months now. So, I just need to focus on my health. I am okay,” he said.
“Remember, after the game of Siwelele, I went to the doctor and they booked me off for 10 days. So, I am strong now.”