Owen decided not to risk an injury to a leg, sustained in training, but the expensive signing from Real Madrid will be fit to play for England in the next round of Internationals next week.
Shola Ameobi, drafted in as Owen's replacement, endured a nightmare match in attack leaving Alan Shearer as an isolated threat.
Newcastle were also without Nolberto Solano, Emre, Kieron Dyer and the result was that Portsmouth spent much of the match in control without being able to turn their pressure into goals.
But the man behind Newcastle's draw was their goalkeeper Shay Given who made a series of top-class saves to deny Portsmouth, who are still looking for their second win of the season.
Graeme Souness was quick to praise Given for his part in Newcastle keeping a clean sheet after some poor defensive performances in recent matches.
Souness said: "Given made at least three top-class saves. He is a top-class goalkeeper and I don't think anyone who knows him would disagree that he is as good as it gets in the Premiership.
"It is hard to say who is the number one goalkeeper but, put it this way, I would not swap him."
While Owen chose to sit out the match, Scott Parker passed a fitness test and got through plenty of hard work in midfield.
Souness added: "I cannot say I am pleased with a draw and, yes, I am disappointed not to have won, but I am not sure we would have deserved it.
"We battled well enough and worked hard and kept Portsmouth in control.
"But without Solano, Emre and Dyer to create some magic we were not the same force. With them I would have expected to win if they had been available.
"I should think the Portsmouth manager must be delighted. His players worked their socks off for him.
"We were sloppy in our passing, but I could not have asked for more from my players and it is a plus that we did not concede any goals."
Given made two fine saves in the first half, keeping out shots from Dario Silva with his foot after 15 minutes and then diving to his left to push away a fierce shot from Gary O'Neil.
But his best saves came in the last nine minutes when a centre from Brian Priske found Matt Taylor unmarked and only six yards out.
But Given made an instinctive reaction save to push the ball over the bar to become an early contender for save of the season.
From the corner taken on the right by O'Neil, Taylor was again unmarked and Given dived to his left to save again.
There was a scare for the Newcastle camp which included more than 1,000 travelling fans when, in the last minute, Given appeared to have brought down Zvonimir Vukic down as the Serbian international attempted to go around the keeper.
But referee Steve Bennett decided Vukic had dived and instead of awarding a penalty produced a yellow card for the culprit.
Newcastle failed to create a single clear opening and Shearer was reduced to taking long-range free-kicks in a bid to break the deadlock.
Portsmouth are still looking for their first home win, but manager Alain Perrin says he no longer fears getting the sack.
Perrin's future was the subject of debate during the week after Portsmouth had suffered two defeats including one in the Carling Cup at League One Gillingham.
Pompey had plenty of possession and produced some neat football but had nothing to show for it, to the disappointment of their largest crowd of the season.
Perrin said: "Keeping a clean sheet when you go away is good news but it is not good enough at home.
"I was worried we might concede a goal at the end when the game became much more open. I decided not to risk it and put on another midfield player.
"I was disappointed we did not win after being in control for so long and our record is not good yet.
"My job is to find a solution to our problems. I am impatient for a win and I hope the Chairman will be patient with me."
Perrin refused to talk about the late penalty incident and was more concerned at the level of performance from his team.
He added: "I would rather play rubbish and win than play well as we did against Newcastle and manage only to draw."
Perrin received criticism from Portsmouth fans for starting the match with only one striker in Dario Silva.
His former Newcastle flair player Lomana LuaLua was recovering from a dose of malaria, while Laurent Robert was denied the opportunity to face his old club because the Football Association would not allow him, as a loan player, to play against his parent club.
Newcastle had Steven Taylor booked for a foul in the second half and Parker got the same for a clumsy midfield challenge as Newcastle battled to hold out.
Pompey keeper Jamie Ashdown had almost nothing to do but he prevented Charles N'Zogbia from scoring a surprise goal in the 37th minute.
N'Zogbia intended to centre from the left, but the ball dipped towards the near post and Ashdown had to change direction at the last second to keep the ball out with his chest.
Man of the Match: Shay Given - Some outstanding saves kept out Portsmouth. No wonder Graeme Souness rates him as the best in the country.