His free-kick headed to the far post where it was not cleared by the rearguard or collected by goalkeeper Ben Williams, leaving Peter Clarke to slot home from three yards amid the melee for his fifth goal of the season. Following the 14th minute opener, the Shrimpers nearly doubled their advantage in the 20th minute, with Francis again the instigator.
The defender latched onto a long Clarke pass and crossed to striker Francis Laurent. The Frenchman's initial effort was parried by Williams and Laurent slammed his second attempt against the left upright, leaving Richard Keogh to clear the danger.
Midfielder Jeff Smith registered the Cumbrians first effort on target, but his shot from distance was easily held by Steve Mildenhall. Southend maintained the pressure with Alan McCormack flashing a 35-yard effort just wide of the post.
Greg Abbott tried to revive Carlisle's fortunes by bringing on Cleveland Taylor on the right wing and pushing Joe Anyinsah to join previously lone striker Danny Graham in a 4-4-2 formation at half-time. The change saw the Cumbrians become more of a threat but saw the game degenerate into a stalemate with no real chances made.
That all changed in the 70th minute when Damian Scannell netted his first goal for the Shrimpers. The winger latched onto a Theo Robinson pass and cut inside before firing the ball into the centre of the goal with his left foot past a shell-shocked Williams.
Alan McCormack completed the win in the 80th minute when his attempted pass to Robinson came back off a defender and the midfielder rifled a shot into the bottom right-hand corner of the goal. Southend went close again late on with Williams parrying an 18-yard effort from substitute striker Lee Barnard before Francis' 25-yard free-kick hit the crossbar.