The pair missed the team's 3-1 win over Cameroon in their tournament opener in Ndola, Zambia on Monday.
Orlando Pirates defender Malepe was suspended, while striker Mahlambi was only recently released by Wits for Amajita's other two pool games.
Senong said: "Before the tournament started we were the only team that came with 19 players. So it was also important for us to have all of our players available. We are happy that we don't have injury issues, we don't have suspension issues and also unavailability issues.
"Tercious is captain and is the leader of the team. Phakamani is also a senior player in the team. We Are happy now we have 21 players and this always gives the technical team a headache in terms of selection. But it is always nice when you have a camp where everybody is fit to play, and that will also help us identify the best eleven to help us in the next match."
Amajita have also been paired with Sudan in Group B, with Group A comprising Zambia, Egypt, Mali and Guinea.
The top four finishers at the eight-team tournament will qualify for the FIFA U-20 World Cup, taking place in South Korea from May 20 to June 11.