First-half goals from Sam Smith and Max Cleworth put the Red Dragons in command, with Smith powering home a header before Cleworth struck from a corner.
Zak Swanson’s deflected effort early in the second half set up a tense finale, but Wrexham stood firm.
But preparations for the home side had been far from ideal.
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"The energy levels weren't quite where they needed to be, we've had a bit of illness in the camp over the last few days," Parkinson said.
"But we just dug deep as a team and we restricted them to very few chances."
Smith, who opened the scoring, was among those affected and failed to see out the match, while Kieffer Moore had also been unwell.
"A few of the lads had it and Sam at half time was feeling ill. Kieffer had already been ill over the last couple of days.
"Sometimes you get that and someone might bring it into the club from home and we'll just clear the building in the next day or two and come back ready to go again."
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Parkinson praised Smith’s impact despite his condition.
The Wrexham manager said: “Sam was really good in that first half. He was one of the lads who had a stomach bug and he was struggling at half-time.
“I said ‘Come on, Sam, another 15 minutes’. He’s been brilliant for us, ever since he’s been here.
“That’s a real old-fashioned striker’s header, a great finish.”
"I thought we were excellent first half. We really bossed the game," Parkinson added.
"Second half, the deflected goal's gone in and we didn't quite get the control we wanted.
"But sometimes football is about finding a way to win and we've done that really well tonight."
“We dug deep and it’s a great win.”
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Portsmouth manager John Mousinho felt his side deserved more.
“The old cliché – a game of two halves. I thought we completely dominated the second half but gave ourselves too much of a mountain to climb, " said Mousinho.
“We were really disappointed with the first goal and the second goal was obviously a set-piece that stemmed from a foul, and the less we talk about that the better.
“I thought there some really poor officiating for the whole night.
“If it had been 1-0 at half-time the outcome would probably have been different.”
The Dragons looked on course for a comfortable victory as Smith and Cleworth headed home in the first half at Stok Cae Ras.
Pompey pulled a goal back through Swanson as they rallied in the second half but, despite applying considerable pressure, were unable to find an equaliser.
After moving back into the play-off places with a frenetic 5-3 victory over promotion rivals Ipswich, and with an FA Cup tie against Chelsea to come, there is much excitement about Wrexham at present.
That was not necessarily evident in this contest as Parkinson’s men began to look leggy and laboured after a bright start but, with another three points, momentum is continuing to build in their favour.
