Imps substitute Guy Ipoua had only been on the pitch three minutes when his header was palmed wide by Blues goalkeeper Darryl Flahavan.
From the resulting right-wing Kevin Sandwith corner, City skipper Ben Futcher leapt up at the far post to head home his second goal of the season from six yards.
But the lead was to last less than 60 seconds before the Shrimpers were back on terms. Lee Beevers brought down Southend man of the match Mark Bentley in the penalty area as he raced in to meet a Duncan Jupp ball.
Referee Clive Penton pointed straight at the spot and booked Beevers for the foul and Peter Gain for dissent. Southend top scorer Freddy Eastwood waited patiently before sending the spot-kick straight down the middle for his 18th goal of the campaign.
It was Eastwood who had the first attempt of the game after 13 minutes, but his 30-yard effort was easily held by City keeper Alan Marriott.
Futcher responded by forcing a smart save out of Flahavan, before new signing Derek Asamoah's prod was safely gathered by the custodian.
Jamie McCombe registered the visitors' last attempt on target, with Flahavan again having the measure of him, before Blues replied with Spencer Prior's header giving Marriott no problems.
The keeper had a lucky escape on 55 minutes when Gower headed an Eastwood cross on target and Marriott held onto the ball at the second attempt.
He also denied Wayne Gray and Carl Pettefer before Lincoln had the ball in the net through Gary Taylor-Fletcher on 62 minutes only for referee Mr Penton to rule the striker's effort out for a foul on Pettefer.
A barrage of Blues shots with 10 minutes to go were beaten away by the Lincoln defence before the grandstand finish.