With Southend out of action due to Sunday's LDV Vans Trophy final, they took advantage to reclaim the top spot.
The Shrimpers drop to second, with the Iron back in third spot - replacing Swansea.
They looked set to hold Lincoln to a goalless draw at Sincil Bank, until Garry Monk's own goal deep in stoppage time gave the Imps all three points.
Chester moved further away from the relegation zone with a 2-1 win over Boston.
Kidderminster's hopes of avoiding relegation took a blow as Bury scored a late equaliser to earn a point in a 2-2 draw.
Rock-bottom Cambridge appear doomed to Conference football next season, but stunned play-off hopefuls Darlington with a 3-1 win at the Abbey Stadium.
Bristol Rovers cruised to a 3-0 win over Bristol Rovers, with Oxford beating Notts County and Rochdale seeing off Leyton Orient at Spotland.
Grimsby and Wycombe played out a 0-0 stalemate at a blustery Blundell Park.
Barnet will play League football for the first time in four years after their 3-1 win over Halifax at Underhill sealed the Conference title.