Tranmere Rovers forward Elliot Nevitt had the ball in the back of the net in the first-half but referee Tom Nield saw a foul on goalkeeper Liam Roberts.
In reality, Nevitt’s goal wouldn’t have made much difference to the result after a dominant second-half performance from the visitors.
A fiesty opening 45 minutes saw an intense outing from both sides.
It even led to both teams exchanging heated words on their way down the tunnel at the break.
Northampton came out of the blocks firing after the interval. There were chances galore for the Cobblers as they ran riot on the Wirral.
They should have had more than the two goals they ended up scoring, with Kion Etete and Paul Lewis both going close.
Sam Hoskins went even closer as a deft chip from the midfielder nicked off the bar and away from danger.
Tranmere were largely toothless in the final third, with Nevitt and Liam Feeney both making a mess of plenty of chances.
Feeney’s decision making was a bit odd all afternoon.
The winger darted into the box from the left and decided to chip the ball to the byline in the middle of his run.
The goals eventually game with Tranmere caught napping at the back.
The first was on the counter with Mitch Pinnock firing in a cross from the left. It deceived the back four and left Kion Etete wide open. He then smashed the ball into the back of the net.
The second came from the penalty spot, with goalkeeper Ross Doohan accidentally tripping Northampton forward Etete.
Sam Hoskins stepped forward and tucked away the penalty beautifully as he put it out of the reach of Doohan into the bottom left corner.
“I don’t want games to be decided by the referees, I want it to be decided by the players.”
In his pre-match programme notes, Tranmere boss Micky Mellon questioned refereeing decisions in midweek. Perhaps he’ll have to do the same following today’s game.
Referee Nield was lenient throughout and seemed reluctant to show a yellow card to either side.
Tranmere will feel hard-done-by as they now drop to eight in League Two.
They travel to face Mansfield next Saturday, in a game that Micky Mellon’s side could really do with winning now.
