Infantino, who is seeking re-election, has faced open revolt after three confederations -- UEFA, AFC and CONCACAF -- attacked his conduct and called for him to quit following his aborted bid to bring private investment into FIFA competitions, including the World Cup.
But Motsepe believes it should be up to all FIFA members to decide whether Infantino remains president at the organisation's 77th Congress in Rabat, Morocco on March 18.
"Elections are taking place next year. We should allow that process to continue and let the 211 members decide," Motsepe told Sky News on Wednesday. "If there are candidates who want to stand against him, put up their names. That's the right thing.
"What I like to focus on is the unity, the cooperation. How do we continue to develop and grow football in the midst of the challenges we have? We must deal with those challenges, resolve them and move on."
Motsepe believes leaders should be open to scrutiny, but says FIFA has processes in place to deal with complaints.
"If I, as a president, behave in a manner that does not reflect due process or governance, I should be subject to interrogation and have those questions asked of me," he said.
"If anyone has got a problem against anybody, whether it's Gianni or anybody else, follow the FIFA process. And if you want to take him out, go for elections. Simple as that.
"Let the 211 member associations decide. The vote will express whether they have confidence in him or not. Everybody is entitled to fair judgement and fair treatment. Everybody should be heard. Due process, governance and legality are non-negotiable."
Motsepe confirmed Infantino still has the support of CAF.
"He's been loyal to African football. He enjoys the support of Africa," he said.