Chuba Akpom grabbed a landmark goal but Middlesbrough missed a chance to turn up the heat on promotion rivals Sheffield United.
Boro's 24-goal top scorer swept Michael Carrick's side ahead midway through the first half with a slick 60-yard counter-attack started and finished by the in-form striker - the Teessiders' 1000th goal at the Riverside.
Akpom could have helped himself to a first-half hat-trick as he fired wide after pouncing on Ben Wilmot's weak back-pass before sending a curling 20-yard effort against the bar.
Mid-table Stoke hit back on the stroke of half-time through Ki-Jana Hoever, the on-loan Wolves defender firing through the legs of keeper Zack Steffen from Josh Laurent's crossfield pass to make it three goals in five days for the Dutch youngster.