Two goals in a nine-minute spell were enough to earn Lincoln their fourth home win of the season.
City were frustrated early on by the Southend defence and it took over an hour to break the deadlock.
But the Red Imps finished on top and their victory pushed them up into fourth place in the Nationwide Division Three table.
A delighted Lincoln manager Keith Alexander said afterwards: "Southend made it difficult for us but we kept our shape and eventually we imposed our game on them.
"I felt we were getting a bit frustrated until we scored. We've been playing reasonably well in recent games without getting the points but today I was delighted with the win."
Lincoln had an early chance when Simon Yeo set up an opening for Simon Weaver but the Lincoln midfielder was denied by a brave save from Darryl Flahavan.
The Southend keeper, who took a knock on an ankle, did well again in the 29th minute when he produced a diving save to keep out a long-range free-kick from Stuart Bimson.
Lincoln finally went in front after 62 minutes when former Tottenham youngster Peter Gain broke down the middle before finishing with a 20-yard left-foot shot.
Southend's defence were caught out again in the 71st minute when Bimson's inswinging corner was headed home by the unmarked Yeo.
The Shrimpers suddenly came to life and Neil Jenkins fired home a 75th minute consolation goal from 25 yards.
Southend manager Rob Newman said afterwards: "I'm disappointed with the way we conceded the two goals.
"If we can't come to a place like Lincoln and get a result we're not going to get anything in this division.
"People might say it's sour grapes but the pitch was disgraceful. It was just like a Sunday morning park pitch and it's incredible that a professional football club are playing on a pitch like that."