Sehrou Guirassy looked as though he had secured a point for his side with an equaliser minutes earlier, but Giroud profited from some poor Rennes defending to claim the win after Callum Hudson-Odoi had put the visitors in front in the first half.
Chelsea top Group E with 10 points from four games, level with Sevilla but ahead on goal-difference, after the Spanish side also claimed a late 2-1 victory in Russia against Krasnodar to seal their passage into the knockout stages.
“I’m very happy to qualify with two games to spare,” said Chelsea manager Frank Lampard. “It was a really tough match, they’re a very good team. Their recent form doesn’t reflect how good they are, it was a tough hard-fought win.”
Rennes, who have one point, had their moments but were largely kept at bay by Chelsea goalkeeper Edouard Mendy.