Goals from Ryan Manning and Richie Towell put Rotherham 2-0 in front, before the visitors earned a share of the spoils thanks to goals from Tom Ince and substitute Bojan.
Millers started with Michael Smith in attack, after the striker shrugged off a niggling injury.
But it was the visitors who had the first clear chance in the fifth minute. Midfielder Joe Allen picked up the ball, before slipping in Benik Afobe, but the striker's low shot was well saved by Marek Rodak.
If that save was routine, Rodak was called into more urgent action 10 minutes later, diving low to deny Afobe.
In between, Millers midfielder Towell saw his low effort deflected wide, while Smith failed to get any power on a close-range header and it was easy pickings for Jack Butland.
Rodak palmed over a volley from Allen, before the Millers goalkeeper saved from Peter Etebo, but the offside flag had gone up.
Afobe was a constant threat for the visitors, and the former Huddersfield Town striker saw his header hit the woodwork before half-time.
But Rotherham stunned the visitors with two goals inside three minutes at the start of the second half.
First, Ryan Manning converted from the penalty spot - after a foul on Ryan Williams.
Then, Richard Wood's header was goal-bound, but Towell was on hand to get the final touch.
Stoke cut the deficit with a Tom Ince goal on 59 minutes, and Allen should have equalised but smashed his volley against the crossbar.
But with five minutes remaining, the visitors made it 2-2 when Bojan's looping header left Rodak stranded.
Despite letting slip a two-goal advantage, Millers manager Paul Warne remained proud of his players for their display.
?He said: “We started the second half really well and probably got two goals too early
”I asked the lads after the game what their overall emotion was and it was disappointment because they got into 80 odd minutes ahead. Mine was of pride because I was really proud of how they played.
”I thought the lads were outstanding. They brought quality on off the bench. We send them out with a smile on their face and they try to compete against some unbelievable players.
”I think they have earned a lot of respect off a lot of people. They give everything they can for this great club and I am hugely proud of them.”
Rotherham: Rodak, Mattock, Vaulks, Ajayi, Wood, Towell, Manning, Newell, Williams, Smith, Jones. Subs: Price, Vyner, Forde, Palmer, Taylor, Wiles, Lewthwaite.
Stoke: Butland, Pieters, Allen, Williams, Ince, Etebo, Afobe, Martins, Berahino, Martina, Woods. Subs: Federici, Adam, Shawcross, Fletcher, Crouch, Bojan, Edwards.