Boro took only 11 minutes to open their 2016/17 account as summer signing Alvaro Negredo climbed highest to head home Gaston Ramirez’s centre.
The former Manchester City striker has now scored with his first shot on target in the Premier League for both of his top-flight clubs.
Aitor Karanka’s side immediately went in search of a second and the woodwork was all that denied the hosts from doubling their lead, Ramirez striking the paint on two separate occasions before the break.
Stoke then capitalised on their good fortune to level proceedings after a slow start to the second period.
After hitting a sighter over the bar from the edge of the box, Switzerland winger Shaqiri found his range midway through the second half with a ferocious free-kick that flew past Victor Valdes to make it 1-1.
See: Middlesbrough's match report