Matthias Kouo-Doumbe continued his goalscoring form from the win over Hartlepool United when he put Town in front after 7 minutes before Timlin levelled for play-off chasing Southend.
Chris Hackett scored the crucial winner on 57 minutes and with Torquay being held at home by Burton Albion it means Northampton are off the foot of League Two and with renewed hope of avoiding the drop out of the Football League.
Having made the most of two consecutive home games it is back to Sixfields again on Saturday when Bristol Rovers are the visitors. They are one of four teams now within six points of Northampton with Chris Wilder's team having shaken up the relegation battle.