James Constable’s 11th goal of the season gave the visitors a lead against the run of play in the opening quarter of an hour.
Rene Howe equalised in first-half stoppage time and Newport’s control on the game was reflected in goals in the final 20 minutes from ex-United players Ryan Burge and Chris Zebroski.
Substitute Alfie Potter pulled one back late on, but United could not claim an equaliser in the dying seconds as they tasted defeat on the road for the first time since going down by the same scoreline at Aldershot on April 1.
Lewis felt his side had got what they deserved.
The caretaker manager said: “The better team won, without a shadow of a doubt, even though at the end we got round the back of them and I think we should have got an equaliser.
“Perhaps we should have nicked a result, although we wouldn’t have deserved it.”
He added: “We said all week Newport was going to be one of our toughest games away from home and they were really on the front foot.”
The decisive moment came eight minutes from time, when a terrible mix-up saw Johnny Mullins and Ryan Clarke gift Zebroski a simple finish to make it 3-1.
For Lewis, it summed up the evening.
“Where two of your most consistent performers in Ryan Clarke and Johnny Mullins make a mistake like that, perhaps it was going to be one of those nights,” he said.
“It’s a great run and we shouldn’t have to change too much.
“Newport were the better side and that happens sometimes.
“You could see the effort the lads were putting in at the end and we were pretty close to getting a 3-3.”
Aside from the result, it was a costly evening for United.
Tom Newey picked up a two-game ban for collecting his tenth yellow card of the season, while Dave Kitson (hamstring) and Danny Rose (illness) were forced off.