Infantino is seeking re-election at FIFA's 77th Congress in Rabat, Morocco, on March 18, 2027, but his leadership has come under increased scrutiny after three confederations, UEFA, AFC and CONCACAF, criticised his conduct and called for him to step down.
The criticism followed Infantino's failed attempt to bring private investment into FIFA competitions, including the World Cup.
However, Motsepe believes the appropriate way to resolve the dispute is through the electoral process rather than calls for Infantino to resign.
"Elections are taking place next year. We should allow that process to continue and let the 211 members decide," Motsepe told Sky News.
"If there are candidates who want to stand against him, put up their names. That's the right thing."
The South African also stressed the importance of unity within world football, urging football leaders to focus on developing the game while addressing challenges through established processes.
Motsepe acknowledged that FIFA leaders must be held accountable, when necessary but insisted that complaints should be handled through the organisation's governance structures.
"If anyone has got a problem against anybody, whether it's Gianni or anybody else, follow the FIFA process," he said.
"And if you want to take him out, go for elections. Simple as that."
Motsepe added that every FIFA member association should have an equal opportunity to express its position through the vote.
"Let the 211 member associations decide. The vote will express whether they have confidence in him or not," he said.
Despite the growing criticism surrounding Infantino, Motsepe confirmed that the FIFA president continues to enjoy CAF's backing.
"He's been loyal to African football. He enjoys the support of Africa," Motsepe said.
