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Danny Rose added a third in injury time to add gloss to the scoreline and ensure that the Cobblers remain in the relegation zone.
Bristol Rovers struck in the final minute of their game against Morecambe, Kaid Mohamed's injury-time goal gifting them a narrow 1-0 victory and putting the Pirates above Exeter City, who lost 1-0 to a Kayode Odejayi-inspired Accrington Stanley.
Dagenham & Redbridge also left it late to score and seize a 1-0 victory over Oxford United, Luke Howell's strike from outside the box allowing his side to claim all three points and possibly mount a late playoff challenge.
In other results, Mansfield Town beat AFC Wimbledon 1-0 in a game marred by bookings, Newport County had two men sent off in their 2-1 defeat against Portsmouth, Southend United beat Torquay United 1-0, and there were goalless draws in the games between Fleetwood Town and Rochdale, Scunthorpe United and Wycombe Wanderers, and York City and Burton Albion.
Results in full: Bristol Rovers 1-0 Morecambe, Dagenham & Redbridge 1-0 Oxford United, Exeter City 0-1 Accrington Stanley, Fleetwood Town 0-0 Rochdale, Hartlepool United 0-1 Cheltenham Town, Mansfield Town 1-0 AFC Wimbledon, Newport County 1-2 Portsmouth, Northampton Town 0-3 Bury, Scunthorpe United 0-0 Wycombe Wanderers, Southend United 1-0 Torquay United, York City 0-0 Burton Albion