Southend grabbed a point thanks to a battling away performance.
United struggled earlier and went behind to an early goal but a controversial refereeing decision handed them a penalty to level things up.
Lincoln's opening goal came in the ninth minute when Michael Blackwood got in a cross from the left that caught the Southend defence cold.
Garry Taylor-Fletcher found himself unmarked and he dived in to put his header past the Southend keeper .
Six minutes later Simon Yeo put Francis Green in the clear but the striker shot straight at Bart Griemink.
Taylor-Fletcher and Simon Weaver then both went close before the game was turned on its head by a controversial decision from referee Garry Lewis.
The referee awarded a spot-kick after Lincoln keeper Alan Marriott appeared to fairly tackle Wayne Gray.
A three-minute delay followed before Gray was able to take the penalty which he dispatched into the bottom corner after sending Marriott the wrong way.
The decision appeared to throw Lincoln out of their stride with Southend almost taking further advantage.
Mark Bentley linked up with Mark Gower but from a good position he sent his shot over the bar.
Lincoln's Yeo had two good chances to settle the game. But first of all he shot over the bar and then he put his effort too close to Griemink.
The game became scrappier in the second half with Southend Drewe Broughton yellow carded for punching the ball away after conceding a free-kick.
He was followed into the referee's book by Lincoln's Blackwood and Southend goal scorer Gray.
Southend snuffed out the Lincoln attack throughout the last 45 minutes but failed to push forward enough to give themselves a chance of all three points.
Apart from their penalty they failed to make a single shot on target.
But seven minutes from time they created a rare chance when defender Nicky Nicolau broke down the left and found Lewis Hunt at the far post but the substitute put his header wide.
Lincoln boss Keith Alexander criticised referee Garry Lewis for the penalty which gave Southend a share of the points. But Alexander admitted his players had themselves to blame for wasting chances.
'It was a very, very poor display from start to finish by the referee.
'I was very disappointed by the penalty decision. Marriott came across and looked to have played the ball fairly. But in the first half we played well. Some of our passing and movement was good but the end product wasn't there.
"Southend defended well but we had enough chances to have won the game."Southend manager Steve Tilson said: "We worked hard. The attitude and desire was there.
"It was a good result for us but we didn't get what we deserved. All credit to the lads. They worked their socks off.
"We made a couple of changes fron Saturday when we lost but the biggest difference was that we played at a much higher tempo. We got the ball forward quicker and it paid off.
"Our two centre halves won everything in the air and the keeper made some good saves. It was a good all-round performance.'