The South African international took his league tally to five goals from eight matches as the Athenians claimed their fourth victory of the campaign.
For his first, the 21-year-old smashed home Lossemy Karaboue’s lay off from outside the box in the 19th minute with his side already trailing 2-0 and the hosts made it 3-1 just before the interval.
He headed home Mehdy Guezoui’s cross from close range shortly after the restart to make it 3-2 in the 55th minute.
Livio Nabab converted 83rd minute penalty before Mothiba completed the emphtic come back by pocking home the winer from close range in the 86th minute.
Mothiba received his maiden call up from Stuart Baxter and is expected to help Bafana return to winning ways with a crucial 2018 World Cup World Cup Qaulifer against Burkina Faso next weekend.