The Egyptian midfielder hasn't featured in a league game since joining Boro in the summer and was limited to 45 minutes in the Carling Cup.
Shawky played his normal role as a holding midfielder but it appeared that he wasn't assigned attacking duties.
Tuncay Sanli scored the winner in the 20th minute after burying a loose ball home from close range.
Shawky's defending abilities and his fighting on every ball helped Boro escape with just their fifth league win in 20 games.
They jumped to 14th spot on 20 points.
The African Cup winner put a shaky performance in the first few minutes but found his form as time went on.
Shawky had an angry argument with England defender Sol Campbell over an off-ball challenge from Portsmouth striker John Utaka, who used to play for Egypt's Ismaili, on a Boro defender.
But the former Ahli star faces a strong possibility of losing his starting place as he will head to Cairo to link up with the Egypt team preparing for the African Cup of Nations in Ghana.
The tournament starts on January 20th and finishes on February 10th.