Wharton sent-off as controversial late penalty costs Cobblers victory at Leyton Orient
Cobblers missed out on a chance to move into the top three in Sky Bet League Two after Josh Wright scored a late penalty in Tuesday's bad-tempered 1-1 draw at Leyton Orient.
Town were just five minutes from a fifth straight victory after Ryan Watson's fizzing first-half finish but Scott Wharton was deemed to have handled in the box, controversially, and Wright made no mistake to deny the visitors all three points.
Wharton then lost his cool and clashed with several opposition players as they celebrated the goal, leading to both him and Orient's James Dayton seeing red as the game ended in chaos.
Unlike on Saturday against Morecambe, Northampton were by some distance the stronger side before half-time and they deserved the lead handed to them by Watson's powerful srike.
But the hosts were better in the second period and came away with a point thanks to Wright's late spot-kick as the game ended in dramatic and farcical fashion,
Cobblers remain sixth but the loss of Wharton for three games, including Friday's FA Cup tie against Championship side Derby County, will be a major blow to manager Keith Curle.
Curle made two changes to his side as Michael Harriman replaced Sam Hoskins at wing-back and Matty Warburton came in for Andy Williams up front.
Cobblers edged the early play and after Sam Sargeant made routine saves from Paul Anderson and Watson, Warburton missed a golden chance to put Town in front with nine minutes played.
Orient made a mess of playing out from the back and Warburton only had the goalkeeper to beat but clattered the woodwork and neither Vadaine Oliver nor Nicky Adams were able to scramble in the rebound.
Wharton headed narrowly over and Watson was a whisker away from reaching Oliver's knockdown inside the box as Town continued to make more of the first-half running, although Orient gradually got a foothold.
It took the home side until the 38th minute to have a shot of any kind and it was a decent chance for Connor Wilkinson inside the six-yard box, but he found the firm palms of David Cornell.
Cobblers were comfortably the better side in the first-half though, and they eventually made their superiority count just moments before half-time. Oliver's flick from a long ball fell to Watson and he delayed the shot before rifling emphatically into the roof of the net.
Orient were marginally improved in the second-half but they were struggling to build up a head of steam in attack as Town defended their lead with relative ease.
Eventually, though, Orient began to turn the screw and were twice close to levelling with Charlie Goode throwing his body on the line to block inside the six-yard box and Cornell reacting well to keep out James Dayton's deflected shot.
Wharton was next to produce a crucial block but the Cobblers couldn't hold out for much longer and Orient were level with just six minutes to play in contentious fashion.
Referee Alan Young penalised Wharton for handball in the box - despite the defender clearly being pushed in the back - and Wright tucked away from the spot.
It all kicked off afterwards as Wharton and James Dayton clashed before nearly all 22 players got involved in a messy brawl. After lengthy consultation with his linesman, the ref sent off both Wharton and Dayton.
Orient then could have won it in stoppage-time, denied only by two fine saves by Cornell as Town were grateful for the point in the end.
Orient: Sargeant, Ekpiteta, Coulson (c) (Maguire-Drew 58), Clay, Happe, Brophy, Harrold (Sotiriou 57), Marsh, Cisse (Dayton 63), Wright, Wilkinson
Subs not used: Vigouroux, Judd, Kyprianou, Sweeney
Cobblers: Cornell, Goode (c), Turnbull, Wharton, Harriman, Lines, Watson, Anderson (Martin 70), Adams (Hoskins 56), Warburton, Oliver
Subs not used: Arnold, Hall-Johnson, Johnston, Roberts, Williams
Referee: Alan Young
Cobblers fans: fg