Paul Sturrock's men triumphed 5-3 on penalties after a thrilling 3-3 draw which saw Tyrone Marsh score his first goal for the club with a close-range header and Sean Rigg and Tom Craddock also find the back of the net.
But after Southend's substitute keeper Dan Bentley kept out Alfie Potter's spot-kick in the shoot-out, Elliot Benyon converted to send Southend through.
Lewis said: "We're very disappointed to go out on penalties, these shoot-outs are always a bit of a lottery.
"They can go either way and we've won a couple of penalty shoot-outs this year.
"It was a cracking game, really open, and I thought we showed good character to fight back after going 3-2 down.
"We had a couple missing and gave young Tyrone Marsh his first start here and he scored a good goal."