In tough conditions, the hosts ran in three tries to the French side's one and now sit on 17 points - one above Saturday's opponents.
The Ulstermen were 10-6 up at the break as Rory Best and Jacob Stockdale touched down while scrum-half Alexi Bales kicked a couple of penalties for the visitors to keep them in touch.
La Rochelle took the lead early in the second period as Bales scored after excellent work by former All Black Victor Vito.
However, Nick Timoney earned the home side a deserved triumph with a second-half score as John Cooney kicked the conversion plus a penalty.
Ulster assistant coach Dwayne Peel was delighted, telling BBC Radio Ulster: "It was a good effort from us. You look at La Rochelle's performances in Europe and what they've done in the Top 14 and they're a real top side, and there was a lot of character shown today in difficult conditions as well."