Tapelo Nyongo sniped the spoils with a penalty in the 87th minute after Ovidy Karuru went down in the box.
Usuthu, who bought the topflight status of NFD champions Thanda Royal Zulu in the off-season, lost the services of Sadate Ouro-Akoriko 13 minutes in at King Zwelithini Stadium.
Ouro-Akoriko re-signed with the coastal outfit in June, having initially left them when they were relegated from the topflight. But it was to be a forgettable second 'debut' for the Togolese defender as he was dismissed after scuffling with his former team.
In the 24th minute ex-Kaizer Chiefs striker Siphelele Mthembu notably made his debut for Ea Lla Koto as he came on for the injured Allen Nono.
The numbers were eventually evened when Stars had Sfiso Mbhele sent off for a challenge on Thembela Sikhakhane in the 80th minute.
Nyongo then struck at the death, as new coach Cavin Johnson claimed a win in his first test since taking over the reins from Zimbabwean tactician Joey Antipas earlier this month.
AmaZulu will visit Chippa United in Port Elizabeth on Tuesday, while Sammy Troughton's charges will host champions Bidvest Wits the next day looking for their first victory under the one-time Stellenbosch FC mentor.