Antony Sweeney gave Carlisle the lead late in the first half only to see Conor Clifford strike back for Shrimpers two minutes later and it was Southend who had the better second-half chances.
John White was inches off giving the visitors a 24th-minute lead when his driven shot flew across the face of goal and past the far post.
Myles Weston and Barry Corr both went close for Shrimpers before Carlisle took the lead against the run of play in the 43rd minute when Patrick Brough swung in a superb cross from the left and Sweeney stole between two defenders to head home from six yards.
It was a short-lived lead because in first-half added time Clifford picked the ball up 25 yards from goal and drilled a low shot which beat the keeper Mark Gillespie's dive.
Dan Bentley twice came to Southend's rescue in the second half, saving a David Symington stinger then defying Jack Marriott in a one-on-one situation. At the other end only Gillespie heroics with a double save kept out Barry Corr and Shaquile Coulthirst efforts.