After a goalless first half it was Rovers who took the lead courtesy of a Raheem Hanley penalty kick after Elliot Wheeler had handled.
But Stoke City hit back with the lively James Alabi heading home from close range.
Lee Williamson came through 86 minutes, but Adam Henley was replaced after sustaining concussion just before half time in a game in which both sides had the chances to claim all three points
Stoke City, managed by former Rovers Reserve team boss Glynn Hodges, started the better of the two sides at a cold and blustery Leigh Sports Village.
But despite their attacking play pinning Rovers back in the opening exchanges, their efforts were well off target.
James Alabi only troubled the roof of the stand with an early shot, whilst a near post effort from Adam Thomas was beaten away by David Raya in the Rovers goal.
Their best chance of the opening half came on 21 minute when Alabi made his way from left to right to shoot from inside the box but again Raya was equal to their efforts.
As Rovers started to impose themselves in the centre of the park, the balance of play shifted their way. Lee Williamson cool and composed when in possession.
On 23 minutes the two seniors, Adam Henley and Lee Williamson, combined well down the right to tee up Dean Rittenberg who laid the ball off for Hugo Fernandez to chase, but a moments hesitation proved costly as Daniel Bachmann was able to make the save to deny the Spaniard.
A minute later and Williamson tested the Potters with a free kick, but Bachmann got across well to save.
Rovers continued to force the pace, a quick break saw them have two on one, but Fernandez opted to shoot instead of squaring the ball to Rittenberg and the Stoke City 'keeper made the save.
Adam Henley had had a quiet return to action but a two minute spell at the half saw mixed fortunes for the youngster.
A great run down the right saw the Welshman beat three, but his cross was cut out, then as the ball was worked inside he gave chase in the area, but as goalkeeper and defender closed in the three collided with Henley coming off the worse.
Henley stayed down but thankfully after a spell of treatment he was helped to his feet and with the aid of the physios he made his way off the pitch with the suspicion of concussion, which was later confirmed as the young defender was sent to hospital as a precaution.
Youngster Sam Lavelle came on to replace Henley for his first Under-21s outing.
The added time for the injury to Henley saw Rovers have two further opportunities as the half drew to a close, both fell to Dean Rittenberg after good work in the box but on each occasion his efforts were blocked.
The young Rovers forward would have the first chance of the second half as he broke through the Potters' back line, but with just the 'keeper to beat Rittenberg's effort was well saved.
But on 54 minutes Rovers were handed the chance to take the lead with with the award of a penalty. A high ball up to Raheem Hanley was controlled well, and as the ball bounced up it struck the arm of Elliot Wheeler and with the referee well positioned he immediately pointed to the spot.
Hanley took the responsibility of the spot kick and made no mistake, cooly slotting the ball into the corner with the goalkeeper diving in the opposite direction for his first of the season.
Boosted by the goal Eric Kinder's side immediately went in search of a second, the impressive Lee Williamson let fly from distance but his shot was saved, then Dean Rittenberg couldn't find a colleague after good work in the box.
But the visitors weren't without their chances either, the fleet-footed James Alabi beat the offside trap to race through but Raya got something on the ball to allow Anthony O'Connor to clear, then Charlie Ward tried his luck from distance, the ball flying just over the bar.
Rovers welcomed back Will Beesley to the fray after he missed the start of the season through injury, but the defender had barely taken up his position at left back when he was beaten by Adam Thomas who sent a dangerous ball over, George Waring couldn't escape the attentions of Anthony O'Connor but the the ball bounced up for James Alabi and he headed home from close range to equalise.
Rovers should have immediately regained the lead as Devarn Green raced through on goal on 70 minutes, but again Bachmann was impressive in one on one situations and got his body in the way of the striker's poked effort.
As the game entered the final stages, the result could have gone either way. With the lively Dean Rittenberg up front for Rovers they always had a chance, whilst Stoke striker George Waring went close with a powerful header that flew over the crossbar.
Lee Williamson came through an impressive 86 minutes for the Under-21s, the midfielder at the heart of everything that was good for Rovers. He was given warm applause as he made his way off to be replaced by Deniz Pero.
Stoke almost stole all three points at the death when Aaron Tumwa sliced horribly but Jamie Ness couldn't capitalise and fired wide from close-range.
It was an entertaining game with a draw just about the fair result.
"I thought we were terrific tonight," said coach Eric Kinder.
"Against Arsenal our backs were against the wall and we didn't play to a tempo, we didn't pass it good enough. I've just said to the lads in there that the way they've trained last week was superb.
"They've now started to move the ball a lot faster, a lot quicker and I thought they got their rewards tonight.
"On chances created I thought we could have pinched it, we had two good chances when the two young lads were clean through, but credit to their 'keeper he has made some decent saves.
"So I'll settle for a point, I thought we were miles better than what we have been."
ROVERS: Raya, Henley (sub Lavelle 44 mins), Bauress (sub Beesley 66 mins), Williamson (sub Pero 86 mins), O'Connor, Tumwa, Fernandez, Paulo Jorge, Rittenberg, Green, R. Hanley.
Subs not used: Urwin, Paul.
Goals: R. Hanley (pen) 54 mins
STOKE CITY: Bachmann, Wheeler, Gomez, Ward, Grant, Keane, Thomas (sub Dawson 90 mins), Ness, Waring, Zapata-Caicedo (sub Rossi 58 mins), Alabi.
Subs not used: Watkins-Clark, Eve, Heneghan.
Goals: Alabi 68 mins.