On loan striker Dean Bowditch gave Northampton a fourth minute lead as the Ipswich player advanced to the edge of the box before beating Gareth Stewart with a deflected shot.
But Bournemouth were back on level terms one minute later when Jason Pearce caught the Northampton defence asleep and Brett Pitman took advantage to score from close range.
Bournemouth seemed content to defend for long periods as Northampton worked hard to break them down.
Poul Hubertz had a great chance after he intercepted a back pass and rounded Stewart but wasted the opportunity from a tight angle.
Hubertz then did well to set up Jason Crowe but he shot just wide with the goal begging and then Bowditch set up Danny Jackman but he in turn shot weakly at the Bournemouth keeper from a good position.
Crowe finally restored Northampton's advantage three minutes before half-time when he found space to head on at the far post after Hubertz did well to turn and get in his cross from a tight position.
Crowe almost grabbed his second a couple of minutes later but was denied by Stewart, who saved at the midfielder's feet.
Northampton carried on from where they left off after the restart with Hubertz seeing his dipping free-kick go just over the bar, before Daniel Jones increased the home side's lead in the 50th minute after beating Stewart with a low drive following a patient build up.
Bournemouth offered little in reply their only chance falling to Danny Hollands, who could only find the side-netting from a good position.
Jones went close again before Bradley Johnson grabbed Northampton's fourth goal in the 67th minute with an accurate shot after the impressive Hubertz had created the opening.
Hubertz should have scored a deserved fifth three minutes later but he headed wide at the far post from a cross by Bowditch.