Mohsni was making his first appearance in nine months after being frozen out with the Shrimpers, but received his marching orders after just 27 minutes for a poorly-timed challenge on Cobblers' winger Chris Hackett.
Before the red card, Northampton had taken the lead in the 11 minute when a long throw from Ben Tozer on the right was flicked on to the far post where former Shrimpers loanee Roy O'Donovan hooked the ball home.
However, the Cobblers were unable to hang on to their lead as, in the 65th minute, Matthew Lund, who was making his debut after signing on loan from Stoke, headed home a right-wing corner from Kevan Hurst.
Southend remained on top after the equaliser with Hurst and substitute Freddy Eastwood both going close to scoring.
But Northampton stole it right at the death with captain Kelvin Langmead heading home from close range as Shrimpers goalkeeper Paul Smith stayed rooted to his line.
