Ivorian striker Sede Junior Dion grabbed a brace as Gallants advanced to the next round of the cup competition.
Speaking after the final whistle, Malesela shared his dissatisfaction with his team's performance.
Kgaogelo Sekgota (South Africa) – 1 cap
Siyabonga Ngezana (South Africa) – 2 caps
Bruce Bvuma (South Africa) – 3 caps
Daniel Cardoso (South Africa) – 3 caps
Dumisani Zuma (South Africa) – 3 caps
Njabulo Ngcobo (South Africa) – 6 caps
Cole Alexander (South Africa) – 6 caps
Lazarous Kambole (Zambia) – 16 caps
Ramahlwe Mphahlele (South Africa) – 18 caps
Lebogang Manyama (South Africa) – 19 caps
Daniel Akpeyi (Nigeria) – 19 caps
Keagan Dolly (South Africa) – 19 caps
Eric Mathoho (South Africa) – 37 caps
Teddy Akumu (Kenya) – 45 caps
Khama Billiat (Zimbabwe) – 49 caps
Bernard Parker (South Africa) – 73 caps
Itumeleng Khune (South Africa) – 91 caps
Scroll through the gallery to see the international players among Kaizer Chiefs' ranks
"I don't know where the minds of our players were at," Malesela said post-match.
"Maybe it was because of the division Santos play in, that probably played a role but also to give credit to Santos who made life difficult for us.
"We also made life difficult for ourselves when we could have just converted our early chances.
"They [Santos] probably played to not lose by a big margin, where we are happy with the 2-0 win which is fine for us."