Siphelele Mthembu replaced the injured Kermit Erasmus up front, with Chris David starting ahead of Mpho Makola in the Citizens midfield.
The Citizens, who came into the match on a decent run of form, looked for a positive start in the earlier exchanges but were unable to get an earlier opener.
Mbombela as such grabbed the lead ten minutes before halftime through Justice Figareido's fine strike past second-choice goalkeeper Sage Stephens.
The Citizens looked to draw level right after halftime, but Tingwenyama weren't giving anything away.
In fact, the home side looked for a second on 63 minutes and found the net through Ndlela but the strike was disallowed for offside.
The visitors, who bowed out of this cup in the quarter-finals last season, appeared to head out at the first hurdle for the first time since 2017 while Mbombela pushed for a second round spot.
In the end, the away outfit bowed out in the first round for the first time since falling to Acornbursh back in the 2016/17 season- the season the club was formed.