Patrick Maswanganyi opened the scoring at the Seisa Ramabodu Stadium after 16 minutes.
Daniel Msendami levelled for Gallants on the stroke of half-time and substitute Jaisen Clifford netted a winner in the second minute of stoppage time at the end of the game.
Pirates wasted a number of chances to kill off the tie in the first half, explained Nduli.
He said in the Citizens: “I think we started the game well and created a lot of chances, but we only managed to score one. With the chances we created, the game should have been done and dusted in the first half. We threw away the three points. We conceded silly goals.”
Pirates have now lost their opening two Betway Premiership matches, after going down 1-0 to Sekhukhune United at the weekend.
They are next in action against Mamelodi Sundowns in the first leg of the MTN8 semi-finals at home on Saturday.
Mamelodi Sundowns coach Miguel Cardoso insists his side will not rely on the away goal they scored in the first leg as they prepare to face Orlando Pirates in the decisive MTN8 semi-final.
Magesi have announced the arrival of two new signings as they continue to strengthen for the current Betway Premiership season.
Abdeslam Ouaddou was pleased with Orlando Pirates' performance as they fought back in their MTN8 semi-final first leg with Mamelodi Sundowns to secure a 1-1 draw.
A late goal by Kamogelo Sebelebele ensured Orlando Pirates remain in contention to defend their MTN8 crown after a 1-1 draw with Mamelodi Sundowns in the first leg played at Orlando Stadium on Saturday.
