The Roots Hall success made it five games unbeaten on the road for Cheltenham and defender Steve Elliott believes his side are becoming harder to beat on their travels.
He told the Gloucester Citizen: "We have been on top a lot away from home this season but we needed to be more ruthless and score the goals to put us out of sight.
"We have scored first in a lot of away games and not managed to get a second.
"Teams in this league are going to find it hard to come back from 2-0 down so it was very pleasing to score twice early on at Southend, which is a long trip and always a hard place to go.
"We managed to go in at the break 2-0 up, which gave us a great platform. We were hanging on at the end, but it was a good, battling performance."
Seb Harris's late goal settled last season's corresponding fixture at Sixfields in favour of the Cobblers.