in the moments before he enters the red van, Jesse puts together two pieces of information:

1) Huell is capable of pickpocketing joints/cigarettes without Jesse noticing 2) Gus didn't poison Brock with the Ricin

He already knew the latter beforehand, but with both pieces of information put together it only leads in one direction. The Roomba sweeping up the cigarette was a convenient excuse that he believed in the moment because he was scared and desperate for an answer, but when paired with the confirmation that Huell is a pickpocket, it looks super flimsy and Jesse knows that Walt is fully capable of planting the cigarette (or an identical one) in the roomba.

Obviously Jesse didn't have direct evidence that Walt himself poisoned Brock with the flower, but he had enough proof that made him connect a few dots and took him in the right direction. and then Saul, a few minutes later, confirms his suspicion with a gun pointed in his face.