After Sunday's last-16 match in Phuthaditjhaba left all square at 2-2 after extra time, Maluti secured a 4-1 win in the penalty shootout to reach the cup quarterfinals.
"We should have wrapped it up in the first half, but I'm very pleased with the all-round performance," said Warriors coach Thami Ngubane.
Warriors, who retained possession for most of the first half, had their best chance in the 37th minute when striker Brice Aka from Côte d'Ivoire drew a brilliant diving save from Maluti goalkeeper Mohlolo Khuse.
Three minutes before the break, the visitors took advantage of their fancied hosts' failure to capitalise when Malefetsane Rankati netted to give the amateur side the half-time lead.
Warriors, however, found some composure in the second period and Kamohelo Mabuya equalised shortly after the half-hour mark.
?Four minutes later, man of the match Aka scored a well deserved goal to put the hosts ahead for the first time in the match, stumbling past Khuse to tap the ball in.
Keeping up the fight, and their dogged determination, Mashale Rantabane's header found the back of the net for Maluti with 19 minutes left to level matters once again.
Neither side managed to break the deadlock in 30 minutes of extra time and the match was decided on penalties.
Maluti eliminated Premiers Soccer League giants Orlando Pirates with a crushing 4-1 win in the first round, and coach Morena Ramoreboli was satisfied with their performance in the knockout competition.
"I believe we've done well, and we could have won if we had scored the opportunities we created," Ramoreboli said.
"We have gained a lot of experience in our two games." – Sapa