The home side wielded the axe after their FA Cup upset by Blyth Spartans, making six changes, and the new-look Cherries side triumphed after goals by Sammy Igoe and debutant Joe Partington late in the first half.
The Shakers were unable to get themselves back into the game as they slipped to only their second away defeat of the season, although they remain second in League Two.
And Knill was unable to bark instructions at his troops having picked up a severe sore throat which left him barely audible.
"It was disappointing and I think we got what we deserved," he said. "I thought Bournemouth played very well but we never turned up.
"We looked lethargic, were second to everything, and consequently you end up losing. On reflection, I'd say Bournemouth played well but we are second in the league and we are there for a reason. We all expect better than that.
Frustrating
"I couldn't say a word to the players, which made it even more frustrating."
Knill is hoping to regain his voice for the Boxing Day clash with promotion rivals Darlington, especially with his assistant Chris Wilder set to take up the manager's job at Oxford.
Wilder has had a big influence at Bury since joining in the summer, as shown by the fact he came on the field after the interval to talk tactics with the players after Knill made a double substitution.
"We decided to change things around at half-time," said Knill. "It was unfortunate that those players came off but sometimes you have to do that.
"It got us going a bit and we were better in the second-half but it wasn't enough to get us back into the game."
BURY: Brown 7, Scott 7, Sodje 6, Futcher 7, Buchanan 6, Bennett 6, Baker 5 (Howell 76), Dawson 7, Jones 5 (Racchi 46, 6), Hurst 5 (Morrell 46, 7), Bishop 6. Subs: Cresswell, Haslam.
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