Pritchard had been rated 50/50 ahead of the game, having played through the pain barrier in the 3-1 defeat to Lincoln City in midweek.
His replacement at Accrington Stanley, Aiden O'Brien, scored a deflected goal within minutes of his introduction but it proved to be a bitterly frustrating afternoon as the ten-man hosts equalised through Mitch Clark late on.
Johnson said it reflected his current squad depth that he has selected the 28-year-old for the last two games.
"It's just the accumulative effect of a few niggles, really," Johnson explained.
"The pitches are heavy at this time of year. It was a renovation project with Alex, both mind and body really.
"I thought he was the best player in the league in December, but for whatever reason it seems to have caught up with him.
"We haven't been able to change it.
"In my honest opinion, we haven't had the personnel to play ahead of a 50% fit Alex Pritchard.
"That's where we are, we've got on with it."
Johnson hopes that having no midweek fixture will allow his team to recover physically, with Corry Evans set to return for Portsmouth's visit.
"I think it will stand us in good stead," Johnson said.
"The market is open, we'll have Corry Evans back and there were no significant injuries from today.
"Then we'll have to go again, and we can't feel too sorry for ourselves."