Wheeler had started Game 1 of the NLCS victory over the San Diego Padres, along with the series-clinching Game 5 on Sunday.
Nola, who had an 11-13 record on 3.25 ERA across the regular season, has not started since being roughed up in Game 2 against the Padres.
Thomson revealed that Wheeler, who has a 3.64 ERA in 10 starts this season when he pitches on four days' rest, will start in Game 2 on Saturday.
"I think the numbers speak to the fact that both him and Nola on an extra day's rest, their numbers are a lot better," Thomson told reporters. "Any time we can give those guys an extra day, we’ll do it."
Wheeler is 1-1 this postseason with a 1.78 ERA and 25 strikeouts, although his fastball velocity dipped on Sunday, yet Thomson endorsed his max-effort strategy.
"I think that's the way to pitch," Thomson said. "You're going to see the top of the lineup in the first two innings, and you better get those guys out or you're going to be in a hole."