Dougie Freedman made an instant impact on his Southend debut but the Shrimpers were denied the points as two goals in 16 second-half minutes maintained Carlisle's unbeaten start.
The veteran striker arrived in a deadline day deal from Crystal Palace on a free transfer and immediately proved his value with a goal.
For a long time that looked like it would be enough to give Southend their first away win of the campaign, but Carlisle refused to roll over and they were rewarded for their industry when Danny Graham scored a 63rd-minute equaliser from the spot and then Cleveland Taylor struck the winner.
The 34-year-old Freedman was a constant thorn in the Cumbrians' side and could have scored after just 18 minutes. On that occasion his drilled, right-footed effort was well saved by Ben Williams.
Williams was forced into action again before the break by Jean- Francois Christophe's long-distance effort.
Advertisement - article continues below »
Gradually, however, Carlisle started to find their feet and after the break Marc Bridge- Wilkinson had a shot blocked.
The equaliser finally arrived just past the hour when Peter Clarke brought down Danny Livesey and Graham scored from the spot.
Then with 12 minutes left the same player turned provider - teeing up Taylor to break Southend's hearts.
