It was a dramatic finish to say the least at the Coventry Building Society Arena, with two red cards and two goals.
North End had just been reduced to 10 men after Liam Lindsay had been sent-off when Emil Riis was brought down in the box to win a penalty.
Sky Blues substitute Fankaty Dabo was shown a red card, leaving it a 10 v 10 game.
Two fans ran on the pitch from the home stands at different times while Daniel Johnson prepared to take the penalty. One was apprehended by stewards but the other evaded capture and went back into the stand.
Johnson scored the penalty to put PNE 1-0 ahead but Coventry equalised with almost the last kick of the game through Fabio Tavares.
What narked Lowe was that a good deal of the stoppage-time was due to the action of the pitch invaders.
Lowe said: "There are lads on that football pitch and anything could have happened to them, those who came on could have had anything with them. It's disgusting.
"I know the stewards try hard but it's a worry isn't it? You can't have people running on the pitch like that.
"DJ did keep his calm but ultimately that might have cost us because of the minutes the referee has put on.
"If I was the referee I would have wanted to get us off the pitch as quickly as we possibly can but he obviously played a bit longer."
Asked whether it was a concern that incidents of fans coming on to the pitch during games was becoming more prevalent, Lowe said: "It will be a concern if something happens, on this occasion we are lucky nothing happened.
"I know fans are passionate and want their teams to win but I just worry about the safety of my players more than anything else.
"When one of the fellas was running on I thought at one point he was going to run right over to DJ or one of my players.
"You think the worse. It can't keep happening."
Not surprisingly, Lowe admitted the last-gasp equaliser had been a big blow to take.
He felt North End would have been worthy winners had they held out.
Lowe: "It was a tough one to take. They put six minutes up and play seven minutes 20, it is definitely tough to take.
"I thought the lads were fantastic in everything they did, coming to place against a team who have been winning games of late, a good team - well coached, well managed.
"But there was one one team who looked like they were going to win it even after we had a man sent-off.
"We got the penalty. I was a little bit disappointed how things went from that, people running on the pitch, threatening players, running around - it shouldn't happen.
"The referee puts six minutes up, probably for that.
"We probably could have done better with the foul for their free-kick, Andrew Hughes slipped and when the ball dropped down the kid scored a great goal.
"If it's six minutes, it's six minutes, It shouldn't be any longer.
"I'm disappointed but the lads were fantastic, they showed real guts and determination to find a goal.
"After we got it we were undone by not their fault if you know what I mean.
"I thought we were well worthy of a win.
"Give Coventry their due, they started well and had a couple of chances. They are a good team but we have come up against a lot of good teams.
"Any other time a draw away from home is very good but not today because we were worthy winners. They stuck to the game plan unbelievably well."