It was the first time since August that 16-goal striker Riis had not made the starting XI for a Championship game.
Cameron Archer and Ched Evans started as PNE's front pair in the 0-0 draw with the Terriers - Riis coming on as a substitute in the 68th minute to replace Evans and Scotty Sinclair taking over from Archer in stoppage-time.
Lowe said: "Emil is carrying a little knock to be fair to him. He didn't train on Tuesday and we have to protect him because he's a goalscorer and a fantastic player.
"When we can mix it up with Ched, Cameron, Emil and Scotty, we have to do that to look after him.
"I think you can see that he has been carrying something over the last couple of games, we have addressed it.
"He will go and see someone on Monday. Emil can still train and play but we won't flog him, we will look after him.
"Was it time for him to have a rest? It looked like he was fine when he came on the pitch.
"Physiologically that might have done him a little favour.
"We'll assess him on Thursday and see how he is for the weekend."
Many people inside Deepdale thought Riis had won a penalty in the 83rd minute when he went down in the box under a challenge from Huddersfield defender Tom Lees.
However, referee Robert Jones - a Premier League official - waved play on, much to PNE's frustration.
Lowe said: "Rob is a good referee, he is a Premier League ref and has worked his way up - he's an outstanding referee.
"It is tough to make those calls, you have to be 100% spot on. He said he will have a look at it but he wasn't 100% sure.
"I will take that as long as when he looks back on it he says it was a penalty.
"The stumbling block was people saying Emil slipped at the same time but Emil says he doesn't slip until his foot catches the stud which then makes him slip.
"It is disappointing. It's not to say we would have scored the pen because we missed one last week - there would have been no guarantees.
"But it would have been nice for the group to get the penalty because they had pushed and worked so hard to get a winner."