Despite missing the heavy defeat to Stoke City two weeks ago, the striker joined up with the Republic of Ireland squad last week, but was forced to withdraw after aggravating the problem.
Even though he was injured, regulations meant Best still had to report to the training camp, but he took part in a session last Wednesday with the announcement of his withdrawal coming hours later.
Although clearly frustrated by the situation, Pardew refused to blame the Irish Football Association, but admitted the player shouldn't have taken part in training after missing a game just days earlier through injury.
Best has already been in hot water with his manager in the last few weeks, with Pardew revealing both he and Stephen Ireland had been disciplined for their nightclub visit 24 hours before the Stoke game.
The 24-year-old will see a specialist on Monday to determine the extent of the injury and the Magpies boss admitted it was a possibility the striker might not return this campaign.
"It's possible (he could miss the rest of the season), yes," Pardew revealed.
"We will have to wait and see. Are we talking weeks or months I have no idea at this stage how long he could be out. When he had this injury before, he had an injection and it seemed to go away but he has had another injection this time and it has not gone away. We might go down the line of having a third injection.
"I would suggest that Leon Best is out for Saturday. That has nothing to do with Ireland's training sessions in fairness to them.
"The injury is such that we have got to get him seen on Monday by a specialist to see exactly what the problem is because it just isn't right. I do not think it was anything to do with extra training with Ireland.''
The Tynesiders will be looking for only their second win in nine games when they welcome Mick McCarthy's side tomorrow but Pardew admits both Jose Enrique and Ireland are both doubtful for the game.
Enrique was forced off in the first half of the defeat to Stoke with a hamstring injury, while Ireland continues his rehabilitation from a groin injury.
The former Manchester City man is yet to make his Magpies debut since arriving on Tyneside from Aston Villa in January, but Pardew is keen to give him extra time to recover.
Cheik Tiote is also missing while he serves a two-match ban for accumulating ten yellow cards, but Joey Barton is fit to take his place in midfield.
The squad returned to training after the international break yesterday, but it was the surprise visit of an ex-England manager that attracted interest at the club's training headquarters at Benton.
Former Middlesbrough and Wolfsburg boss Steve McClaren was a guest at the club for the day but Pardew immediately refuting suggestions he could be joining his backroom staff.
With Pardew looking to re-invest the £35million received from Andy Carroll's in his squad, and McClaren's experience across Europe, the Magpies boss admitted he had been discussing potential targets with the former FC Twente boss.
"He just asked me if he could come in. He just wanted to see what we are doing here," Pardew explained.
"It was like myself. I went to Manchester United and Swansea and other places when I was out of work. You just want to keep in touch and see what is going on.
"I asked him what the Dutch league was like, this player and that player. And in Germany too. I got some great information from him and that is purely it.
"I am not that close to him but he is someone who comes from my era and we have been on the same coaching courses together.
"It was just nice to see him as he was in good shape and is obviously wanting to get back in the game. I hope he does get back soon."