كتب : Hatem Maher
Ryan Shawcross scored Stoke's winner six minutes from time with a fine header.
Egyptian midfielder Shawky was included in Boro's starting line-up and played full 90 minutes after months of uncertainty over his future.
The 27-year-old was quoted last month as saying that he wanted to leave Middlesbrough due to lack of first-team opportunities.
Coach Gareth Southgate said he was not concerned by Shawky's comments but it seems now he still has a future at the Riverside.
Middlesbrough lie second from bottom in the league table with 27 points, four adrift of safety.