Skipper Ben Gibson rescued a point for Stoke as Millwall’s four-match winning run ended at the Bet365 Stadium.
The visitors led at the break through their first attempt on target. Femi Azeez’s low ball across the edge of the six yard-box sneaked through to Josh Coburn, who bundled home from two yards.
Stoke had strong claims for a penalty waved away when Jake Cooper pulled back Wouter Burger as he shaped to slot in from point-blank range.
But the hosts deservedly levelled when Gibson flicked in a near-post header from Bae Jun-Ho’s corner - the first goal Millwall had conceded in five matches, after a run of four straight 1-0 wins.
A fifth draw of the season extended Millwall’s unbeaten run to seven matches, while Stoke have lost just one of their past eight under boss Narcis Pelach.
Milwall’s miserly defence kicked off on the back of four successive clean sheets, but should have conceded after just 25 seconds when Million Manhoef’s whipped low cross found Tom Cannon free at the far post and the striker skewed a shot wide.
Bae’s low 20-yard strike drew a full-stretch save from Lions goalkeeper Lukas Jensen as Stoke enjoyed more than 70% possession in the first half, but they generally struggled to fashion clear openings.
Millwall’s threat grew as the half went on, with Azeez firing into the side netting before teeing up Middlesbrough loanee Coburn for his second Lions goal - and the first since his debut.
After failing to penalise Cooper’s pull back on Burger, referee Will Finnie further fuelled the home fans ire when he handed the Dutch defender his fifth yellow card of the season - and an upcoming one-match suspension - for his protests.
Stoke fed off the added intensity, with Gibson scoring for the second home game running as Millwall conceded only the sixth goal in their past 13 outings.
Azeez almost found a winner for Millwall when he angled a low shot inches past the far post, while Eric-Junior Bocat fired a decent Potters chance over the bar late on.
Stoke City head coach Narcis Pelach told BBC Radio Stoke:
“It’s a penalty for us, a red card, and then probably we win the game, so I’m disappointed.
"It would have been a great week with three wins, but we have to take the point, it is what it is, and don't get frustrated.
“They (the officials) got it wrong. It’s clear, everyone has seen it. The job of the referee is not easy, we are all human beings and we make mistakes.
“They have apologised for the mistake. I have been in charge for 10 or 11 games here and it has happened three times to me now.
“I accept the apologies. We’re all human beings, I’m okay with that, it is what it is, and then hopefully one day it will go the other way.”
Millwall boss Neil Harris told BBC Radio London:
“It’s an excellent point. The whole ground, and probably the whole football industry, thought ‘Millwall are 1-0 up, that’s how it’s going to finish’, but Stoke are a good side in a good moment.
“They caused a lot of problems in the middle third all game, but I think we had the better chances, so I’m delighted with a point.
“Ultimately it’s not just one game - I look at the week and the seven points in a week.
“For us to play Burnley and Leeds at home and come to Stoke, a ground where we’ve not done great at for a long time, it’s a fantastic week for us.”