Mako has impressed in his first season in the PSL with 18 appearances for the Chilli Boys.
However, he struggled with the pace and trickery of City hat-trick hero Bhongolethu Jayiya in the 4-1 loss at Athlone Stadium on Monday.
“No player becomes a bad player after just one game,” Malesela told his club's website.
“I am not the one to judge a player after just one performance. He had done very well for us until the Cape Town City game.
“He has come up against some of the best wingers in the league, and not once he was shaken.
“It was not his day on Monday, and that happens in football,” said Malesela of the ex-Cape Town All Stars winger.
Chippa, in 10th place on the table with eight games left, next face Polokwane City in a Nedbank Cup last-16 tie at Nelson Mandela Bay Stadium on Saturday (15h00).