Flavio Silva opened the scoring at the Mbombela Stadium after just seven minutes.
Khetukuthula Ndlovu levelled on the stroke of half-time but Wandile Duba came on in the second half, for an injured Da Silva, to win the game with goals in the 56th and 66th minutes.
Reflecting on the game, Mongoya praised his players but admitted his team was second best to a decisive Amakhosi.
"I think it was a decent start," Mongoya told SuperSport.
"Congratulations to Kaizer Chiefs, they know how to be decisive in the final third.
"We failed to convince today.
"I was proud of the performance in certain moments, but in the final third you have to be able to play the dangerous passes, which is where they were more composed."
Kruger are next in league action against away to Marumo Gallants on Tuesday 11 August.
Luke Baartman was delighted to be recognised for his performance with the Man of the Match award in Kaizer Chiefs' 3-1 Betway Premiership win over newly promoted Kruger United.
Kaizer Chiefs head coach Fernando Da Cruz was delighted to start his Premier Soccer League career with a positive 3-1 win over league newbies Kruger United.
Half-time substitute Wandile Duba scored twice as Kaizer Chiefs came from behind to beat newly promoted Kruger United 3-1 in their Betway Premiership clash at Mbombela Stadium.
The Betway Premiership has no shortage of exciting young talent, and the 2026/27 season could see several emerging stars establish themselves as household names.
