However, wins at home to Crewe Alexandra, Notts County and Grimsby Town, and an away 1–1 draw at Exeter City lifted Newport into the play-off places after five games had been played.
The following two games away at Port Vale and Oldham Athletic were also won, further improving County's league placing to 2nd, missing out on the top spot on goal difference.
In the next game, Newport suffered a surprising home six–nil loss to Yeovil Town, dropping to 3rd place, but still within the automatic promotion zone.
After briefly rising to 2nd again following the home win against Cambridge United, County consolidated their position in 3rd place until the loss to Crawley Town put them back into the play-off zone.
However after the loss away to Northampton Town in the 36th game, County spent the rest of the season unbeaten, rising up the table back into the last play-off spot.
Into the last three minutes of the final game, both Colchester and Stevenage were winning, Exeter were being held to a draw and Newport were losing at Morecambe.
Newport's next penalty kick was taken by Matty Dolan who made no mistake and booked County's place in the play-off final.
When it looked certain that this game would also go to penalties, Connor Jennings scored for Tranmere in the last minute of extra time to give them the win and promotion to League One.
The draw for the third round had been made before the replay had taken place, with the winners rewarded with a home tie against 2015–16 Premier League champions Leicester City.
Newport had conceded an equaliser at exactly the same late stage in the previous season's fourth-round match with Tottenham Hotspur, but this time they found an even later winner.
Leicester's Albrighton conceded a penalty for handball, which was duly converted by Amond, to put Newport into the fourth round for the second season in succession.
The draw for the fifth round had been made before the replay had taken place, with the winners rewarded with a home tie against Premier League champions Manchester City.
Manchester City had won both their previous FA Cup games 7–0 against Rotherham United and 5–0 against Burnley, but they found County a much sterner test.
Newport kept the scoreline to 0–0 at half time, but shortly after the break Leroy Sané scored for the visitors, but their expected goal rush never materialised.