The summer signing tapped in from a Ruben Rodrigues cross three minutes into the second half, to ensure United maintained their 100 per cent winning start on home soil.
Des Buckingham made four changes to the side which beat Preston North End 3-1 before the international break, with Joe Bennett and Matt Phillips out due to injury, and both Sam Long and Rodrigues dropping to the bench.
Elliott Moore returned to the heart of the U’s defence, while Greg Leigh replaced Bennett at left back. El Mizouni came in for Rodrigues, while Siriki Dembele occupied one of the wide roles.
The opening 45 minutes were light on clear chances, with the majority of efforts coming from range.
With 12 minutes on the clock, Mark Harris, recently crowned the Sky Bet Championship player of the month for August, found space 20 yards out and drilled a low effort down the throat of Viktor Johansson in the Potters goal.
Tyler Goodrham then drove a tame effort at goal from 30 yards, but Johansson claimed it comfortably.
At the other end, Potters centre half Ben Wilmot saw an ambitious swerving strike from 35 yards caught by Jamie Cumming.
The clearest sight of goal came when Potters right winger Million Manhoef spotted Bae Jun-ho in space at the back post on the other side, and played a lovely ball through the eye of the needle to the South Korea international, who blazed over.
After half an hour, a slack free kick inside his own half from Lynden Gooch was played across the pitch to Goodrham on the left, who got a shot away from 25 yards, but Johansson palmed it away to safety.
Dembele was causing problems down the left-hand side, and with seven minutes to go until the break, he left three defenders behind, but overhit his ball across the penalty box.
In stoppage time, Buckingham was dealt an injury blow, when Cameron Brannagan was forced off, and Rodrigues came on to replace him.
Three minutes into the second period though, Rodrigues laid on the assist for El Mizouni to open the scoring.
The Portuguese playmaker received possession on the right-hand side, and played a low ball across the face of goal for El Mizouni to tap home from close range for his first goal in United colours.
The U’s had their tails up and sensed a second goal. A searching ball from left to right saw Ciaron Brown find Harris, who had a lot to do with defenders around him, but he tests Johansson from 20 yards, with the keeper fisting the stinging strike away.
Momentum slowly but surely swung towards the Potters though, and with 20 minutes to go, there were a few hearts in mouths when Manhoef’s cross was played into the gloves of his own keeper at close range by Moore.
With quarter of an hour to go, Buckingham brought Will Vaulks on for Josh McEachran, and four minutes later, a counter-attack led by Dembele, saw the winger feed Harris, who nudged the ball on to Goodrham.
The 21-year-old received the ball in the right channel of the box, and forced a save out of Johansson, who tipped the ball over for a corner.
A great chance was presented to Peter Kioso inside the six-yard box, when the ball dropped to his feet, but he fired over.
Malcolm Ebiowei replaced Dembele for the final eight minutes, and he twice tested Johansson in quick succession with low drilled efforts inside the box.
Four minutes of injury time were signalled, and United were able to see them out and claim another three points on the board.
Oxford United (4-3-3): Cumming; Kioso, Moore, Brown, Leigh; El Mizouni, McEachran (Vaulks 75), Brannagan (Rodrigues 45+2); Goodrham, Harris, Dembele (Ebiowei 82).
Unused subs: Ingram, Nelson, Long, Sibley, Dale, Scarlett.
Booked: None.
Stoke City (4-2-3-1): Johansson; Tchamadeu, Wilmot, Gibson, Bocat; Sidibe (Koumas 58), Burger (Thompson 74); Manhoef, Gooch (Moran 33), Bae Jun-ho (Tezgel 74); Cannon (Ennis 74).
Unused subs: Bonham, Seko, Phillips, Dixon.
Booked: Tchamadeu.
Referee: Dean Whitestone (Northamptonshire)
Attendance: 11,507 (TBC visitors)