Chippa edged Ezenkosi courtesy of a Lerato Manzini goal in the second half to advance to their first ever cup semifinal, despite a nervy end to the match.
Malesela explained that their plan was to wear down the Cosmos defence in order to exploit the gaps better in the second half, but admitted they were shocked at their resilience towards the end.
"We thought the Cosmos players would get tired," he told SuperSport TV. "We thought we would stretch them a little bit more in the first half so we can use their tiring players to find gaps.
"But it wasn't to be – a very good game from them, also a bit of a scare right at the end with them having half chances. But good luck to 'Bra J' [Sono] and the boys for the league.
"Well done to our boys, I think we did well and I think we deserved the win."
Having made five changes to his side from their previous match against Kaizer Chiefs, 'Dance' revealed he had to issue threats during the half-time break to get a better response from his fringe players.
"I actually had to threaten to take some of them [new faces] out at half-time, hence the [Zaphaniah] Mbokomas – the level of performance was upped; [Tshwarelo] Bereng – the level of performance was upped.
"Lerato struggled a little bit today, but it's not bad. If other people can come in and do the job then it's okay for us.
"Now the focus should be on Tuesday already and we need to transfer this into the league."
The Chilli Boys will welcome Maritzburg United to the same venue on Tuesday evening, as they look to gnaw their way back into the top half of the Absa Premiership table.