Yeovil captain Terry Skiverton scored a late winner to end Northampton's six-match unbeaten run.
The home side dominated the first half with Andrew Kirk going close on several occasions to open the scoring.
Northampton had little to offer in attack and did not muster a shot on target until 85 minutes.
But in injury time, Skiverton moved up from the back to rifle home a left-footed drive which gave the Glovers their first win in nine games.
Yeovil: Flinders, Peltier, Skiverton, Guyett, Jones, Kirk, Rose, Bridcutt, Barry, Peters (Williams 75), Owusu (Church 68).
Subs Not Used: Warne, Alcock, Stieber.
Goals: Skiverton 90.
Northampton: Bunn, Johnson (Hayes 71), Hughes, Gyepes, Little (Dolman 52), Crowe, Jackman, Coke (Burnell 81), Holt, Gilligan, Hubertz.
Subs Not Used: Dunn, Akinfenwa.
Booked: Little, Hughes.
Ref: Paul Melin (Surrey).