Lewis has been a regular pick in midfield for Wanderers since moving to Adams Park on loan from Dagenham last season and then signing a permanent deal in the summer.
The 24-year-old made his debut from the bench in November 2010 but has since started every game - barring injury or suspension.
However, he found himself in the unfamiliar surroundings of the substitutes' bench against Tranmere on Saturday
Following the 2-1 home win over Rovers in League One, Waddock said: "Stuey is a very good player and I rate him very highly so he has no worries.
"In many ways, he is unfortunate. He had an illness early in the season and he played very early on after that. He took a whack last week and I just wanted to give him a rest because he puts his body on the line every week."
