The Cod Army went ahead in the second minute through Alan Goodall and then saw Gareth Evans miss a 37th-minute penalty.
They were made to pay five minutes before the end as Barry Corr headed an equaliser, much to Alexander's frustration.
"I'm disappointed to draw the game because I thought we were in control for most of it," he said.
"But playing two games in three days really hit us hard and that showed in the last half hour of the match when Southend found their way back into the game.
"Paul Smith made a great save to keep the penalty out in the first half which obviously proved costly in the end but everyone worked their socks off and we just didn't have the energy levels at the end as the fixture list hasn't done us any favours.
"With that in mind, I'm proud of what the players showed because it would've been easy to feel sorry for themselves but they showed determination before just running out of steam at the end."