The former national team goalie, who was sacked by Bidvest Wits just before the start of the season, takes over from Augusto Palacios signing a three year deal.
Bucs chairman Irvin Khoza says the decision behind Njenje's stepping down is for him to concentrate on his health.
"Mr Augusto Palcios had to go hospital to do surgery on his spine," the Iron Duke says.
"So we have agreed with him that for the benefit of the club, he'll step aside and take time to recover."
"When he's fully recovered, he'll go back to the development team. And maybe sometime in the future he'll help with the first team."
Khoza adds: "The decision was purely based on the health matter and had nothing to do with results."
Palacios says he is sad to leave the job, but that he must put his health first.
"For me the most important thing after the operation is my health and my family. It's very sad to leave the team at this moment."
De Sa says he is happy to be at the club.
"It's an honour to be here. This kind of opportunity only comes once in a career," he says.