The three points sees Boro leapfrog The Potters in the Championship table after a gutsy performance on the road.
James McClean looked to force the breakthrough for the home side, firing in from the byline and forcing George Friend into a smart clearance.
McClean came close again minutes later, hooking a cross goalwards and bringing a strong save out of Boro stopper Dejan Stojanovic.
Set pieces dominated the early stages of the game in blustery conditions at the bet365 Stadium, and after a series of Stoke corners it was Boro who took advantage and seized the initiative.
Patrick Roberts swung in sweet a free-kick from Boro’s right and number 11 Ashley Fletcher was on hand to bag his 11th goal of the season, getting up well and glancing in for the first goal of the Neil Warnock era.
Striker Fletcher then looked set to add to his tally when he pounced on Dael Fry’s knock-down, but Jack Butland made a brilliant point-blank stop with the linesman’s flag up for offside.
On the stroke of half-time, Boro surged forward again as goalscorer Fletcher latched onto a pass from Djed Spence down the right. He stripped his marker James Chester for pace before cutting back to George Saville. The midfielder’s effort was sliced into the air, and Britt Assombalonga appealed for a penalty as he was bundled to the floor by a combination of Potters defender and goalkeeper.
Into the second half, which began with another big opportunity within the first 20 seconds, this time for the home side. The ball came across Boro’s box to substitute Tom Ince at the far post, he left it for James McClean but Stojanovic made himself big and produced a second crucial save of the match.
Minutes later and the woodwork saved Boro, McClean again the dangerman but directing his effort onto the post.
Boro regrouped and came again, Neil Warnock’s first change paying immediate dividends.
Marcus Tavernier, taking his first touches after replacing Patrick Roberts, worked the ball onto his left foot and drilled deliciously into the bottom corner from range.
With our advantage doubled, Boro dug in to see out the victory against a frustrated home side, tensions bubbling over as Nick Powell saw two bookings within the space of a minute to receive his marching orders.
Dael Fry made amends after a rare lapse at the back from Marvin Johnson, clearing off the line in stoppage time to preserve Boro’s clean sheet.