Leyton Orient's promotion bid suffered a setback after they crashed to their second defeat in three games. Orient started brightly but Northampton took the lead on 14 minutes when Giles Coke latched onto Poul Hubertz's flick to finish coolly from 18 yards out.
A last-gasp tackle on Adam Boyd denied the visitors a certain equaliser while Paul Terry also went close for Orient.
The hosts created the better chances in the second half and Hubertz scored from the spot after Jason Crowe was fouled.
Northampton: Bunn, Little, Hughes, Johnson, Jackman, Crowe, Burnell, Coke (Holt 89), Jones, Hubertz, Gilligan (Henderson 80). Subs Not Used: Akinfenwa, Dunn, Hayes.
Booked: Gilligan, Henderson, Bunn.
Goals: Coke 14, Hubertz 78 pen.
Leyton Orient: Nelson, Oji (Purches 53), Mkandawire, Saah, Daniels, Chambers, Terry, Thornton (Melligan 43), Demetriou (Corden 64), Barcham, Boyd. Subs Not Used: Morris, Echanomi.
Booked: Oji, Chambers, Melligan.
Att: 5,405
Ref: Jarnail Singh (Middlesex).
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