Watson sat the last quarter with his hamstring iced however coach James Hird said the substitution was purely precautionary.
"Jobe had a problem in the pre-season (with his hamstring) and we think it is similar. We don't think it is a strain, but we won't know until we have a scan," Hird said.
"If he is fine and there is no strain, we will bring him back."
Watson's substitution was typical of a no-risk policy Hird said the Bombers had adopted since losing Courtenay Dempsey and Jason Winderlich to knee injuries within a quarter during the match against Carlton earlier this year.
"We felt, five goals up at three-quarter time, we could probably bring in (substitute) Travis (Colyer)," Hird said.
Essendon did not require their captain anyway, thanks to a second-half surge that set up the 36-point win.
However, the Bombers struggled to kick goals against Brisbane in the first half, despite holding a 39-17 advantage in forward 50m entries.
"The second quarter, we had a lot of entries, we just couldn't kick the goals and that had a lot to do with the way they were defending," Hird said.
While Hird's Bombers are flying, Brisbane coach Michael Voss is feeling the pressure with his side winless so far this year.
The Essendon coach empathised with the man he shared Brownlow honours with in 1996.
"I think you feel for any coach (in his position). It is a tough job and he is a quality football person," Hird said.
"I am glad they (Brisbane) didn't turn it around this week but I hope they do next week."
Henry Slattery and Michael Hurley were late withdrawals for the Bombers, with a tight hip and tight calf respectively.
Hird said Hurley would be in doubt for next week's match against Richmond.
