The centre-half lasted only 20 minutes of the 3-0 loss at the City Ground before being replaced by Jordan Storey.
Bauer felt a stretch on the Achilles tendon which he ruptured last year.
That needed surgery and seven months out to repair, hence no risks were taken when he felt a niggle this time.
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He was badly missed, the three goals conceded coming after his substitution.
PNE head coach Frankie McAvoy said: “Pat’s Achilles was a bit sore.
“It was one we had a little bit of concern about before the game but Pat said he was fit and ready to play.
“He just over stretched it and it’s the one he had the injury with last year.
“It’s not as serious as the last one but he felt it when he over stretched and we couldn’t take chances with him.
“The disappointing thing is that when Pat went off we conceded three goals.
“He’s done fantastically well for us and it was a blow when he went off.
“We hope the international break gives that bit of time for him to recover, so too Ched Evans and Matthew Olosunde, who have been out.
“The couple of weeks between games gives us a bit of time to work on Pat.”
Alan Browne missed the game with a back injury, while Sean Maguire was only deemed fit enough to be named on the bench.
Like Bauer, Maguire had some soreness in the Achilles area. While named as a sub, any involvement would have been a short cameo.
As it was, the Irish striker was not used.
McAvoy used Daniel Johnson and Brad Potts in support of Emil Riis, Potts putting PNE’s best chance of the game high over the bar in first-half stoppage time.
Said McAvoy: “We went with DJ higher up, he was the one doing the job which Sean normally does – sinking to get on the ball.
“Pottsy was playing against Ryan Yates in the middle of the park and trying to break beyond.
“We were working on Sean and Alan right up until the morning of the game, trying to get them right.
“Sean went on the bench and if the game had gone a bit differently, perhaps he might have been able to do a few minutes.
“But we had Scotty Sinclair on the bench who was fit and a goal threat, so when we changed things we put him on in a front three.
“It was a disappointing day for us, we didn’t play well and the three goals we gave away were poor ones. We didn’t create enough chances.”