Adam Nowland kept Wimbledon in the FA Cup with a 25-yard wonder goal to cancel out John Eustace's early effort.
But the home side will be wondering why they aren't in the fourth round after a host of chances went begging late on.
Wimbledon's equaliser came after they missed a string of opportunities late in the game having pegged Stoke back into their own half for long periods.
Patrick Agyemang and Wayne Gray were the worst culprits after they missed three excellent chances to draw level following some excellent build-up from Jobi McAnuff.
But Nowland was alert enough to curl the ball past Neil Cutler with 18 minutes left on the clock to earn the Dons a replay at Britannia Stadium.
And Nigel Reo Coker was denied a close-range winner six minutes from time by an excellent save from Cutler.
Eustace broke the deadlock on 12 minutes with a powerful volley from Marcus Hall's cross.
The goal came a minute after Carl Asaba was denied by the goalpost, following a spell of sustained pressure by the Potters.
Wimbledon failed to register a shot on target until 25 minutes into the match, when Small's effort was just parried clear by Cutler.
The City keeper looked equally shaky on 33 minutes when Small very nearly got past him only to have the ball taken from his feet.
Cutler apart, Stoke dominated proceedings throughout much of the first half, and Wimbledon's opportunities were restricted to long-range shots on the break.
Wimbledon were fortunate not to score an own goal ten minutes after the break when Rob Gier's clearance ricocheted off Mikele Liegertwood's legs just wide of the post.
But the home side rallied around the hour mark, and Agyemang wasted a great chance when he sliced across the face of goal after blasting into the side netting a minute earlier.