Hughes was sacked after a miserable 10 months in charge of QPR in 2012, but looked to be on course for all three points on his first trip back to the west London club thanks to a goal early in the second half from another former Rangers employee, Peter Crouch.
Crouch, who spent the 2000-01 season at QPR, struck in the 51st minute after Steven Caulker had levelled Mame Biram Diouf’s early opener on the stroke of half-time.
However, Kranjcar rescued Harry Redknapp's side from a fourth Premier League defeat of the season with a superb 25-yard free-kick two minutes from time.
Redknapp looked set to endure a miserable day, with a lacklustre performance capped off by his captain Joey Barton and midfielder Jordon Mutch having to be substituted after returning to the team having missed last week's 4-0 defeat at Manchester United through injury.
However, Kranjcar intervened late on to earn the ex-Tottenham boss a valuable point.
Stoke showcased their counter-attacking prowess in a shock 1-0 win at champions Manchester City in their previous away game, and QPR failed to heed that warning as Hughes' men - inspired by the outstanding Victor Moses - hurt the Londoners on the break throughout and were unfortunate not to take all three points.
QPR controlled the opening stages without really threatening Asmir Begovic's goal, and Stoke punished them after 11 minutes when Diouf broke the deadlock.
Moses bamboozled Mauricio Isla before sending in a quality lofted delivery from the left, and former Hannover man Diouf was on hand to nod home Crouch's towering knock-down from three yards.
Barton's enforced substitution appeared to have made QPR’s task even tougher, but Caulker's first goal for the club drew Redknapp's side level shortly before half-time.
Mutch sent in a corner to the back post, which Caulker headed across goal and into the net via a wild attempted clearance from Charlie Adam.
QPR failed to build on their equaliser after the interval, though, and Crouch - a player Redknapp admitted he wanted to sign in the transfer window in the build-up to this match - restored Stoke's lead six minutes into the second half.
The hapless Isla was robbed in possession by Moses, who picked out Crouch with a low cross that the 33-year-old fired unerringly beyond Robert Green from 12 yards.
Erik Pieters - who overcame a knock to start for Stoke - should have given the visitors some breathing space shortly after following more good work from Moses, but could only scuff his shot at Green from just inside the area.
QPR laboured in their attempts to get back into the match, but Stoke’s defensive resilience - and their ever-present threat on the break - meant the home side struggled to get a clear sight of Begovic's goal.
That was until Kranjcar stepped up from 25 yards to arc the ball over the wall and beyond Begovic's despairing dive to ensure the spoils were shared.
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