Kris Commons headed the Parkhead side into the lead in the sixth minute before he was carried off on a stretcher just before the break with what looked like an ankle injury after clashing with team-mate Beram Kayal.
Hoops midfielder Victor Wanyama, back from suspension, was shown a straight red card 10 minutes into the second half for a challenge on McGowan, who levelled from the spot with 10 minutes remaining after Parkhead defender Emilio Izaguirre was adjudged to have fouled Esmael Goncalves inside the box.
While Celtic will contend that the sending-off and penalty were both harsh, Saints could claim they were unlucky not to have all three points.
The Paisley side had the ball in the net in the first half from a Gary Teale cross only to have it ruled out for Paul Dummett's challenge on Fraser Forster and then had a decent penalty appeal turned down moments from the interval when the ball appeared to hit the arm of Hoops stand-in skipper Georgios Samaras.
However, at the end of an exhausting afternoon perhaps a share of the spoils was fair to both sides on a day when the officials were less than convincing.
In tribute to St Mirren's League Cup final win over Hearts at Hampden a fortnight ago, the visitors gave a guard of honour to the Buddies players.
Neil Lennon made two changes to his side, Wanyama and Samaras were reinstated with Anthony Stokes dropping to the bench and Mikael Lustig out altogether.
Buddies boss Danny Lennon kept the same starting XI which won at Hampden while new signing, Estonia midfielder Sander Puri, was on the bench.
With Rangers chief executive Charles Green watching from the main stand, Celtic started with purpose and even before they got the opener the Saints goal was threatened.
In the third minute Kayal played in Gary Hooper but the Celtic striker's drive from inside the box cleared Craig Samson's crossbar by a yard.
Even so early in the game there was an air of inevitability about Commons's goal which came when Saints failed to clear properly a corner and the midfielder leapt to head in Efe Ambrose's lobbed cross past Samson.
The goal shook the home side out of their early slumber.
Forster had to rush out in the eighth minute to save from Paisley defender Dummett, who had been sent through by McGowan, but the corner was easily defended.
Moments later St Mirren midfielder Conor Newton's speculative drive from 25 yards flew over the bar before Commons missed the target at the other end with a header.
In the 13th minute Kayal was perfectly placed to clear Marc McAusland's header from a Teale corner off the line and moments later, Thompson headed a Teale cross past the far post.
Still Saints kept coming forward with growing confidence, with Teale the danger man.
In the 27th minute his looping cross from the left saw Dummett challenge with Forster at the back post with Izaguirre in close attendance.
The ball ended up in the net but referee Bobby Madden blew for an infringement on the keeper, to the anger of the home crowd.
A competitive encounter continued apace and almost 10 minutes later Celtic had another chance but Hooper fired over the bar from 12 yards under pressure from McAusland and Dummett.
Celtic suffered a blow just before the interval when Commons was taken off the field on a stretcher after injuring himself in a clash Kayal under pressure from Goncalves.
There was time for an unsuccessful but valid Saints penalty appeal when Teale's deep corner from the left hit Samaras on the arm and the half-time whistle blew with the Buddies players and fans raging.
Saints supporters were appeased to an extent when the cup was paraded at the interval but Celtic, with Stokes having replaced Commons for the start of the second half, showed renewed vigour when play resumed.
That enthusiasm made way for a sense of injustice when Wanyama was sent packing for his challenge on McGowan in the centre of the park.
The game was in danger of boiling over for a few minutes but Celtic re-organised as St Mirren pushed for the equaliser.
Dylan McGeouch replaced Hooper in the 70th minute but 10 minutes later Saints got the chance to level from the spot when Izaguirre challenged Goncalves and McGowan confidently knocked the spot-kick past Forster.
With three minutes remaining and St Mirren sensing a victory was there for the taking, the impressive Teale drove just over from the edge of the box.
In injury-time Forster caused a moment of panic in the Celtic defence when he fumbled substitute Graham Carey's cross but there was to be no more scoring.