After playing for Liverpool, Real Madrid, Newcastle and Manchester United, the 33-year-old announced in March he would hang up his boots after just one season in the Potteries.
Owen's final appearance came away at Southampton, coming on for the final 16 minutes of a hard-fought 1-1 draw on the south coast.
The striker was given a standing ovation by all inside a sold-out St Mary's and, despite having failed to make a league start for Stoke, boss Pulis praised the influence he has had at the Britannia Stadium.
"It was always the plan to bring him on," he said. "He had a great chance in the second half to actually put the icing on the cake.
"If he had scored, I think even the Southampton supporters would have given him a round of applause.
"He got a great reception and he deserves it. He has been a very, very good pro for us and, not just his football side, he is a very, very good family man.
"We're pleased with the year he has been with us. He is good fun to work with, a good person to work with and we wish him all the best for the future."
While Owen can concentrate on a career in the media and his growing horse racing empire, the future of Pulis and chairman Peter Coates is less certain.
Pulis was coy on that after the match and also about the training ground incident that marred the build-up and led to an internal investigation.
Kenwyne Jones smashed team-mate Glenn Whelan's car windscreen in a mistaken act of retribution after he found a pig's head wrapped in his clothes.
Jones did not travel to the south coast to face his former club, while Whelan continued to miss out through a groin injury.
"We kept Kenwyne and Glenn away because of that distraction," Pulis said.
"We didn't want to bring any distraction on the players, we wanted to focus on the game. I think we've done that.
"I've spoken to the two lads, they understand. I've had a good chat with them. It was a prank and everybody knows that.
"I think it's been a week of the lads getting at it in lots of respects.
"We'll deal with it in house and then the club will let you know. I have to say the disappointing thing is some coverage has been poor.
"One newspaper said it was about religion. That had absolutely nothing to do with it whatsoever.
"You have to accept it and get on with it. I'll speak to Peter and the family and let you know. As soon as we've sorted it all out we'll let you know next week."
Southampton's immediate future looks a lot more settled after executive chairman Nicola Cortese ended speculation about his future by announcing he would stay at the club.
Saints manager Mauricio Pochettino had pledged to follow the Italian out of the club and is pleased the situation has been resolved.
"I think that Nicola Cortese staying is the best possible news for next season," the Argentinian said.
"That is very good for the squad, for the whole club. We will talk about the summer and the budgets with Nicola from tomorrow [Monday]."
Fans chanted the names of Cortese and Pochettino throughout a match which Southampton could count themselves somewhat unfortunate not to win.
City went ahead through a Peter Crouch header two minutes into the second half, before Rickie Lambert levelled 10 minutes later.
The fine form of Stoke goalkeeper Asmir Begovic prevented Saints going on to win the match, meaning they end the season without a win six attempts.
"We wanted to win, but weren't able to do so," Pochettino added.
"The same story has happened, we dominated, created better chances, but we just couldn't close down the game and it shows we need to be more clinical and assertive."