A Nathan Collins header secured the points for the Potters during a low-key affair. The hosts enjoyed the best of the first half with Chuba Akpom coming close to doubling their lead with an own goal.
Boro sprung into life during the closing five minutes of the half with George Saville hitting the post. It was as good as it got for the lacklustre Teessiders, who had plenty of possession without any punch in the second half.
City could have made it more comfortable for themselves with Morgan Fox and Tyrese Campbell wasting good chances. Stoke were dealt a blow when skipper Sam Clucas was subbed on eight minutes after failing to shake off an injury following a Sam Morsy challenge.
The injury, and two spells of treatment, disrupted the flow of the game with both sides struggling to settle inside the opening 15 minutes. An unmarked Collins headed City ahead after Fox picked him out at the back post on 19 minutes.
James McClean fired a tame effort straight at Marcus Bettinelli on 24 minutes. Bettinelli palmed away a mis-directed Akpom header, before saving James Chester's follow-up three minutes later.
Marvin Johnson's cross-shot was saved low at his near post by Joe Bursik on 34 minutes. Bursik cut out another dangerous Johnson cross along the face of his six-yard box two minutes later.
The Stoke keeper got down well to keep out a deflected Johnson shot on 39 minutes before George Saville hit the outside of the post from the rebound.
Fox lacked composure and skied an effort over from the edge of the box after Campbell set it up on 49 minutes. Bettinelli spread himself well to block a Campbell shot after Nick Powell's slide-rule pass opened the defence on 51 minutes.
Johnson had another decent cross cut out by Bursik on 60 minutes after Boro players failed to gamble on the near post. Campbell was booked for throwing the ball away on 69 minutes before Saville was booked for a studs-up challenge on Powell.
Campbell had a shot saved by Bettinelli on 73 minutes after Jonny Howson missed the ball completely. Jacob Brown went into the book for a late lunging tackle on 79 minutes.
Campbell fired high and wide from a tight angle as the game began to get stretched. Dael Fry had a goalbound shot brilliantly blocked at close range by Chester on 80 minutes as Stoke comfortably held on.
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