The Clever Boys had taken a tough stance on their prized asset last week when Mahlambi was called up to the Amajita squad for the youth championship finals.
Wits CEO Jose Ferreria initially refused to allow the 19-year-old to travel to the camp as "the competition does not fall under the FIFA calender".
SAFA CEO Dennis Mumble then threatened sanctions against the club, as he emphasised that national teams take precedence over club commitments.
While Thabo Senong's troops left for Zambia on Friday, Mahlambi remained with his club for their Absa Premiership clash against Mamelodi Sundowns on Saturday, when he came on in the second half of their 2-0 defeat at Loftus Versfeld.
However, an agreement has since been reached between the national association and the Milpark-based club that will see the School of Excellence graduate link up with the Amajita squad for their remaining two group games.
“The player will join the national team," Mumble told TMG Digital. "We’re just trying to get him on a flight so he can go [on Monday].
"Obviously he’s not going to be able to play in the first game [against Cameroon tonight]."
“We had told [Wits] we had two options. The first was to regulate the release of players going forward for every single national team.
“But we said don’t want to do a rigid system‚ but rather work with the clubs so the clubs can also succeed.
“So there was give and take and we still want to work with the clubs on an individual basis – sometimes we need them and they need us."
Amajita will play their final Group B clash against Sudan on Sunday, March 5, after which Mahlambi is expected to immediately return to his club, ahead of their CAF Champions League first round, first leg clash away to Al Ahly on March 11.
“They have released the player today [on Monday]. If he can, he will go today. If not, he will leave first thing in the morning [on Tuesday]. He has to be back with them for their Al Ahly game," added Mumble.
Should South Africa progress through the group stage of the eight-nations tournament, they will earn a place at the 2017 FIFA Under-20 World Cup in Korea in May, which Mumble says is the main objective for Senong's side.
"Our main priority is to reach the U-20 World Cup‚ and we will know from the first round whether we have qualified for that.
“After that‚ we will still aim to win the competition‚ but our key objective would then have been met,” he concluded.