Former QPR boss Hughes appeared set to take three points off his old club when another Loftus Road old boy – Peter Crouch – restored Stoke’s lead until Kranjcar curled home an equaliser with two minutes left.
Stoke took the lead on 11 minutes when Crouch climbed above Rio Ferdinand to knock down Victor Moses’ cross and Mame Biram Diouf stooped to head beyond Robert Green.
Crouch was in the thick of things and he inadvertently contributed to QPR’s equaliser three minutes before half-time when he and Charlie Adam got in each other’s way as they tried to clear Steven Caulker’s header, with the ball eventually being sliced into the roof of the net.
But Crouch then made a positive impact at the right end of the pitch six minutes into the second half when he swept home Moses’ cut-back from the left.
A flurry of bookings seemed set to mark a scrappy conclusion to the game until Kranjcar whipped a brilliant free-kick over the wall and beyond Asmir Begovic’s reach to salvage QPR a point.
Hughes – sacked following a testing 10-month spell in November 2012, after which the west London club slipped to relegation amid financial turmoil – was expecting plenty of abuse from the home supporters, and it was only a few minutes before chants against the former QPR boss rang around Loftus Road.
The Welshman has, though, steadily rebuilt his reputation at Stoke, whom he guided to an impressive ninth-placed finish last season, and Hughes was pumping the air as his side went ahead.
The ball was played out to Moses on the left, and his lofted cross was headed down by Crouch, who held off former England team-mate Ferdinand, and Diouf nodded it past Green.
The visitors remained a threat on the break, but Diouf chose the wrong option when shooting at the edge of the penalty area when he had men over on both sides.
Crouch was then unfortunate not to make it 2-0 after another quick break when played in by Moses at the edge of the penalty area. He took the ball in his stride before drilling a low effort just wide of Green’s right-hand post.
At the other end, Kranjcar fired a 25-yard effort just over the angle of post and bar.
QPR captain Joey Barton, whose inclusion was one of four changes to the side beaten 4-0 at Manchester United last weekend, had to be replaced because of injury, with Matt Phillips coming on.
The home side were level just before the break. A corner from Jordon Mutch on the left floated over to Caulker at the back post. His header down into the crowded six-yard box was toe-poked up into the Stoke net.
QPR were forced into another change just after the restart when Mutch hobbled off, replaced by Karl Henry, and Stoke regained the lead in the 51st minute.
Moses, on loan from Chelsea, caused problems down the left, squirming to the touchline before cutting the ball back into the box.
Crouch, who had been linked with a summer move to QPR, dropped off Ferdinand, which gave him the time and space to fire a left-footed shot past Green for a first Premier League goal in 10 games.
Stoke should have sealed victory on the break when Adam picked out Steven Nzonzi arriving in the right side of the penalty area, but his side-footed effort was wide.
QPR felt they should have been awarded a penalty when Stoke captain Ryan Shawcross appeared to pull Caulker’s shirt, but referee Martin Atkinson was not interested.
With eight minutes left, there was a flashpoint as Shawcross clattered Kranjcar with a late sliding challenge, with Leroy Fer squaring up to the Stoke captain.
Eventually, the referee booked both players, which did not go down well with the frustrated home support.
Loftus Road was, though, soon rocking when, after being fouled by substitute Steve Sidwell, Kranjcar clipped a free-kick up over the wall into the top right corner, past the diving Begovic.