Colchester United slipped to their second defeat of the season in Sky Bet League Two as Amond wins the game for the hosts after a late Jevani Brown eqauliser.
The U's named a team with two changes from the side that came out on top against Harrogate Town at the weekend.
Jevani Brown and Kwame Poku were replaced from the starters by Courtney Senior and Luke Norris.
The U's were on the backfoot for the opening twenty minutes, with Gerken twice forced to save from Tristan Abrahams. County's first effort was easily collected by the U's 'keeper, before he was tested more with a curling effort from a tight angle on the edge of the penalty area.
But when Gerken was beaten, the bar came to the rescue for Colchester United. Scott Twine's dipping free kick from thirty yards out rattled the bar before Tom Eastman was able to clear the lines for the U's.
Abrahams went close again for the hosts with half an hour played, latching on to a cross from Haynes from the right wing. But the tricky forward was unable to keep his effort down from inside the six-yard area as the ball rocketed harmlessly over Gerken's bar.
The U's best chance of the first half came when Miles Welch-Hayes and Courtney Senior combined down the right flank. Welch-Hayes played in Senior who sent in a fiendish cross with Luke Norris attacking at the back post, but just unable to connect with the ball.
The half drew to a close with the score goalless.
But the hosts wasted no time in the second half when Scott Twine fired his side in front. From a short free kick, he ran the ball towards goal before unleashing a powerful shot that blasted in to the top corner giving Dean Gerken no chance.
And Newport looked to have their tails up at the start of the second half. Tommy Smith put in an important interception with Padraig Amond lurking in the centre of the area.
Steve Ball reacted with a double change for his side with Jevani Brown and Kwame Poku coming on and replacing Luke Norris and Harry Pell.
Brown got himself straight into the action when he combined with Callum Harriott. From a chipped ball, Brown chested the ball down to the oncoming Harriott who ran the ball towards goal before testing Townsend in the home goal with a powerful drive.
The U's kept pressing a strong home defence, with neat play around the edge of the area, but struggled really test Townsend in goal for Newport.
But with two minutes of normal time to play the U's had their breakthrough.
Kwame Poku's swerving shot was spilled by Townsend with Jevani Brown following in and tapping the ball home from inside the six-yard area to the unmanned goal.
Steve Ball and his men thought they had snatched a point from the league leaders, but Newport showed why they are top of the table when the game entered injury time. A corner sent to the back post was nodded over the line after a scramble by Padraig Amond to win the game for the Exiles.
Colchester United were unable to perform any more heroics with another goal, as the referee blew for full time and the score at 2-1, consigning the U's to their second defeat of the season.
The travelling side slipped to eleventh in the Sky Bet League Two table after defeat, remaining on thirteen points, while the hosts maintained their two point gap at the top with twenty-two points.
Next up for Steve Ball's side is a home match against Stevenage next Tuesday, where Alex Revell's side will come to the JobServe Community Stadium for a 7pm kick-off.
Newport County starting XI: Townsend, Haynes, Demetriou, Dolan, Cooper, Shephard, Labadie (Bennett 85'), Sheehan, Twine, Amond (Ellison 90'), Abrahams (Willmott 90').
Subs: King, Baker, Webb, Proctor.
Colchester United starting XI: Gerken, Welch-Hayes, Bramall, Smith, Senior, Pell (Poku 59'), Norris (Brown 59'), Harriott (Bohui 77'), Chilvers, Eastman, Stevenson.
Subs: George, Sowunmi, Scarlett, Gambin, Bohui.