Kenny Jackett had one changed enforced, as midfielder Craig Clay continued to nurse an ankle injury sustained at Scunthorpe United – with skipper Pratley returning to the side.
Northampton were forced into two changes, with Max Dyche replacing Jon Guthrie in defence, whilst Rose came in for McWilliams.
Orient started brightly, Tom James nearly opening the scoring with a fantastic free-kick.
Right-footed, it looked destined for the top corner, but Cobblers’ keeper Roberts was equal to it, denying the Welshman his 5th of the season.
Roberts was tested again, this time Aaron Drinan trying to find the net again, but the angle of the shot worked against him.
With 20 minutes gone, Kion Etete was forced to withdraw for the hosts, with Nicke Kabamba replacing him.
As the half advanced, Orient looked as if they would be the team more likely to open the scoring; Harry Smith meeting Archibald’s cross, but not able to guide his header goalwards.
Kemp then went close, after a ball into feet was controlled well and then struck, but just past the post on this occasion.
With half-time approaching, it was the Cobblers who would break the deadlock, a long throw in the undoing for The O’s.
It was Pinnock’s throw, flicked on by Dyche, and stabbed home by the onrushing Hoskins to give the home side the lead going into the break.
The O’s looked to start the second half quickly, and pushed high up the pitch, almost forcing an equaliser after pressing high and winning it back in the box.
Drinan’s eventual low strike, however, was once again calmly collected by Roberts.
Jackett soon opted for changes, with Sotiriou and Wood called into action, replacing Archibald and Drinan.
The two nearly combined right away, Wood cutting in to find the forward, but Sotiriou’s long range strike was over the bar.
Northampton threatened on the break numerous times, as Orient tried to break them down, but the hosts ended up more likely to add a second.
In the end, The O’s couldn’t equalise, and left Northampton empty handed.
Northampton Town: Roberts, McGowan, Sowerby, Horsfall (C), Hoskins (Ashley-Seal 90′), Lewis, Pinnock, Koiki, Etete (Kabamba 20’), Rose, Dyche.
Subs unused:, Connolly, Pollock, Flores, , Tomlinson, Maxted.
Leyton Orient: Vigouroux, James, Smith, Kemp (Omotoye 90′), Archibald (Wood 63’), Mitchell, Drinan (Sotiriou 63’), Pratley, Beckles, Ogie, Kyprianou.
Subs unused: Byrne, Happe, Thompson, Papadopoulos
Yellows: Kyprianou 52’, Wood 90′