The 28-year-old handed in a transfer request last week, and following a meeting with the Amakhosi management on Monday, the club decided to consider an offer that was tabled by the Brazilians.
The Amakhosi later ordered Lebese to train with the youth team as negotiations between the two clubs continued.
Football manager Bobby Motaung said the they decided to sell Lebese after he expressed his desire to leave the club.
“The deal was concluded this afternoon. We’ve seen Lebese grow with us and we released him at his request. We are happy that the negotiations went well and an agreement has been reached with Sundowns,” Motaung told the Chiefs website.
“Kaizer Chiefs do not stand in the way when the players express their desire to leave. It’s our policy. We thank Lebese for his contribution to the success of the team and wish him all of the best in his future endeavours,” concluded Motaung.
Sundowns confirmed the news on their Twitter handle, but later removed the post.
The African champions can now register Lebese for the knockout stages of the 2017 Caf Champions League. The dealine for additional players is on Friday.
Meanwhile, Amakhosi also announced that Zimbabwean attacker Michelle Katsvairo will spend the new season on loan at Tanzanian club Singida United FC.
Katsvairo recently turned a loan move to Township Rollers of Botswana.