The Ukrainian hosts dominated the first 45 minutes and should have gone ahead midway through when Andriy Yarmolenko blazed wide with the goal at his mercy.
Having weathered the storm, the Potters took the lead 10 minutes into the second half when Cameron Jerome finished from Ryan Shotton's cross, but after Oleksandr Aliev had hit the bar for Dynamo, Ognjen Vukojevic levelled in stoppage time.
Stoke boss Tony Pulis - whose side have kept six clean sheets already this term - will be disappointed to see a goal conceded at the death, but overall, it was an impressive point to gain from a testing encounter, and a result which extends the team's unbeaten run to nine matches.
Pulis handed Jerome his debut for the club and fellow transfer deadline day recruit Wilson Palacios was also in a Potters first XI showing eight changes from Saturday's Barclays Premier League victory over Liverpool.
Kenwyne Jones came into the attack, with record signing Peter Crouch - the other man to join the Staffordshire outfit just before the transfer window closed - one of several players who had not made the trip to Ukraine.
Another, Asmir Begovic, was replaced in goal by Thomas Sorensen, while the hosts' starting line-up featured former Chelsea striker Andriy Shevchenko.
Pulis sent out his side in a defensive formation and they soaked up plenty of pressure in the opening stages.
Shotton did loop a long throw into the box in the fifth minute that was claimed by goalkeeper Oleksandr Shovkovskiy, but otherwise it was one-way traffic, with Goran Popov, Yarmolenko and Denys Garmash sending shots off target.
Shevchenko then took a short corner and played a one-two with Milos Ninkovic before rifling an effort wide.
Dynamo should have made it 1-0 in the 20th minute when Sorensen parried a fierce strike from Popov, but Yarmolenko could not convert the follow-up from close range.
That seemed to stir the Potters a little and Shotton drilled wide after the hosts failed to clear a corner.
Dynamo were soon back on the front foot, though, with Ninkovic shooting into Sorensen's arms and Shevchenko thumping a free-kick into the Stoke wall.
The home side went close again just after the half-hour mark when Artem Milevskiy's drive bounced off Sorensen, but the Dane dived to catch the ball at the second attempt.
In a rare chance at the other end Jones was unable to get much power on a header from Glenn Whelan's free-kick and towards the end of the half, Stoke's frustration began to show as they picked up a flurry of bookings.
Salif Diao had already been shown a yellow card and three of his team-mates - Ryan Shawcross, Matthew Upson and Robert Huth - followed suit in the space of four minutes before the referee blew the whistle for half-time.
The visitors looked brighter after the restart and Jerome won a corner which Whelan saw punched away by Shovkovskiy.
Dynamo fired a warning as Milevskiy's shot whistled wide, but in the 55th minute Stoke were in front as Jerome marked his first appearance for the Potters with a goal.
Jones released Shotton down the right and the youngster's cross was missed by Shovkovskiy, arriving at the feet of Jerome, who calmly dispatched it into the roof of the net.
The hosts responded by surging forward and Sorensen was called upon to deal with efforts from Shevchenko, substitute Aliev and Popov.
Shevchenko then latched onto a delivery over the top but lifted the ball too high.
Dynamo continued to press and were inches away from an equaliser when Aliev cracked the ball against the crossbar from outside the area.
Jones almost found himself through but was denied by a last-ditch tackle and Shevchenko played a pass square across the six-yard box which substitute Ideye Brown could not make contact with.
It seemed Stoke had secured the victory and there was even time for Jones to fire in a shot that Shovkovskiy saved.
But Dynamo were not done and in the final seconds pulled a goal back as Vukojevic stabbed in Yarmolenko's cross at the back post.