The only goal of the game was in the 74th minute when Antonio Sumbane found the back of the net for the visitors.
Bafana dominated possession in the early stages with Kamogelo Sebelebele going close to breaking the deadlock in the opening 10 minutes.
Mozambique though were always a threat going forward and and it took a Ime Okon clearance to keep the score goalless while Sumbane was denied by home goalkeeper Thakasani Mbanjwa.
The home side were guilty of being wasteful, particularly in the final third of the pitch, with several passes not finding the man and shots off target.
The Mambas eventually made the hosts pay when Sumbane slotted home a rebound after Mbanjwa made the initial save.
Bafana were given a penalty with 10 minutes remaining but the Video Assistant Referee came into effect and the decision was overturned leaving the home side staring at defeat.
Bafana's next encounter in the group will be on Saturday when they take on Zimbabwe.
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