Mike Flynn scored twice for Newport as Richie Barker's first game in charge of Portsmouth ended in defeat.
Newport rode their luck during the first half with Patrick Agyemang's effort cleared off the line.
Midfielder Flynn scored his first goal in 13 months, firing into the roof of the net to give Newport the lead.
Flynn added a second three minutes later with a close range finish to secure Newport's second away league win of the season.
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Portsmouth boss Richie Barker told BBC Radio Solent:
"Speaking to people who've been here a while, they've pretty much said that sums up the season in 90 minutes, so we've got a lot of work to do.
"At the minute it's probably too easy to score goals against us so we need to stop that very quickly. We're in a constant uphill battle so we need to prevent that very quickly and the only way we can do that is by working hard, constant hard work, constant training, trying to do the right things and hopefully people will buy in to what we're doing.
"I'd have to say apart from the first 10 or 15 minutes I thought we were pretty much the best team. We had weathered the storm a little bit, we'd had some really good chances, we probably had the most shots - I don't know the statistics but probably had the most shots - but it's the same old story again."
Newport County first team coach Wayne Hatswell told BBC Radio Wales:
"It was a tough place to come and the boys have been absolutely superb. It's nice to come away with a 2-0 win and a clean sheet as well.
"We've had some good performances on the road and probably not got what we've deserved but our home form has obviously been really good.
"It sets us up nicely hopefully for Christmas and give the lads a bit of confidence after back to back defeats in the cups."
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