In a game that had no implications on the final standings of Group K with Proteas having already locked up first place and Rostov knowing they had no chance of claiming second to earn a last-eight spot, the Cyprus giants prevailed for their fifth win in six games.
Rostov (2-4), who have just appointed Slovenian Sašo Filipovski as their new coach, tied the game at 42-42 with a Fred House dunk.
Proteas went on a 9-2 run over the last three minutes of the third quarter for a 51-44 advantage and they kept the pressure on in the fourth.
Their biggest lead came when Vujadin Subotic nailed a jumper for a 63-46 advantage.
Rostov chipped away at the deficit but ended up losing by 14.
Goran Jeretin had 14 points, with both of his Proteas teammates Subotic and Haris Mujezinovic contributing 13.
Rawle Marshall led Rostov with 13.
Dragan Raca, coach Proteas EKA AEL:
"We didn't start the game seriously. Because we have the Cyprus Cup final only two days ago I had to change the starting team. We played good defense in the second half and we managed to win the game."
Szymon Szewczyk, payer of Lokomotiv Rostov:
"I agree with my coach. I want to wish good luck to Proteas EKA AEL for the next games in EuroChallenge. We are looking forward to the Russian Lleague now."
Goran Nikolic, player of Proteas EKA AEL:
"We played two important games in a few hours. We played a good second half and we won this European game. We are looking forward to the next game in the Quarter-Finals."