Substitute Jake Kirby netted in the 63rd minute to hand the Merseysiders a 2-1 victory which lifted them out of the League Two relegation zone.
Marc Richards continued his excellent season with an equaliser to Kayode Odejayi's opener but it was not enough to prevent a fifth straight league defeat for Northampton.
Having begun 2014 battling to save their Football League status, 2015 promises little difference for the Cobblers with Chris Wilder's team currently just two points off the drop zone.
The only consolation is that their bad run of form is coming now, with plenty of time left to turn things around and the January transfer window for Wilder to continue the rebuilding job that he initially started so successfully by guiding the Cobblers to safety in his first few months in charge.
Speaking to BBC Radio Northampton he said: "I've told some of the players that they are free to go. Some of their agents have done outstanding jobs to get them contracts here.
"We're trying everything, but ultimately losing five games in a row, I understand the nature of the business."