Liam Lawrence got the winner as Stoke extended their unbeaten run in the Championship to seven games. Ryan Shawcross headed in Lawrence's corner with just eight minutes gone.
Shawcross and Richard Creswell then missed chances to increase Stoke's lead before Danny Granville crossed for Clive Platt to head Colchester level.
But Stoke hit back midway through the second half as Ricardo Fuller laid a great pass across the penalty area and Lawrence fired into the top corner.
Stoke boss Tony Pulis:
"We knew it would be a tough week with away games at Leicester and West Brom and then playing Colchester. "But the effort and commitment of the players had been first class.
"Dominic Matteo typified that because he was at a friend's funeral the other day. I had to move him to centre-half and he just got on with it."
Colchester boss Geraint Williams:
"I'm very disappointed. We had spoken about Stoke being a big and physical side and I stressed the importance for us to make a strong start. "But Stoke won their battles and we conceded an early goal.
"I've got a lovely bunch of lads but they have got to start games on the front foot and be more aggressive."
Stoke: Simonsen, Wright, Shawcross, Matteo, Wilkinson (Dickinson 42), Cresswell, Delap, Eustace, Lawrence (Sweeney 90), Fuller, Sidibe (Parkin 67).
Subs Not Used: Hoult, Pericard.
Booked: Lawrence.
Goals: Shawcross 8, Lawrence 73.
Colchester: Gerken, Duguid (Balogh 33), Baldwin, Virgo, Elokobi, Granville (Guy 77), Jackson, Izzet, Yeates, Lisbie, Platt.
Subs Not Used: Davison, Guttridge, Connolly.
Booked: Balogh, Guy.
Goals: Platt 58.
Att: 12,395.
Ref: Clive Penton (Sussex).
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