Ché Adams netted in either half as Southampton came from behind to progress in the Carabao Cup on Nathan Jones's St Mary's debut.
Lincoln gave their fans the dream start, taking the lead after just two minutes as Saints keeper Gavin Bazunu tried to punch clear a miscued clearance, only to find his own net.
Saints’ leveller came on 24 minutes after a spell of pressure. Moi Elyounoussi’s cross met by the head of Adams, who guided the ball home from inside the penalty area.
The hosts certainly looked the stronger of the two sides during the second 45 but had to wait till the 74th minute to take the lead. Adams tapping home from close range after Lincoln failed to clear.
Southampton's new manager named a strong side for his first in charge in SO14, the headline being a return for Kyle Walker-Peters after injury.
World Cup internationals Mohammed Salisu and Armel Bella-Kotchap were also in the eleven, as Ainsley Maitland-Niles partnered skipper James Ward-Prowse in the middle.
The positive news for travelling Lincoln was a place for top scorer Ben House, who recovered from a knock on Tuesday night.
With just two minutes on the clock the visitors were gifted the lead at St Mary’s in front of the Chapel Stand.
A corner floated in from the left-hand side was met by a miscued clearance from Ainsley Maitland-Niles, which caused Bazunu to scramble.
The Saints keeper, under pressure from O’Connor, failed to properly connect before punching into his own net.
Saints’ response was laboured, as the visiting Imps continued to cause problems on the counter.
A drilled shot from Moi Elyounoussi on 16 minutes gave the returning Saints hopeful some hope, before the Norwegian then crafted another opening.
His through ball six minutes later set Adam Armstrong and Adams in on goal. The former looked to lay the ball off for Adams, whose eventual shot was saved by the legs of keeper Carl Rushworth.
Elynounoussi continued to be involved and soon helped Saints back on level terms. His deft cross was met by the run of Adams, who headed beyond Rushworth with 24 minutes played.
In the ascendency, Saints looked to turn this game on its head before the interval, thwarted in the most part by the linesman’s flag as they entered the final third.
But as the break loomed it was Lincoln who should have been ahead; a neat move started by House on the right flank saw Charles Vernam force Bazunu into a low save.
At the interval Jones made a switch, Bella-Kotchap being replaced by Duje Ćaleta-Car.
It was his other centre-back though who almost produced the spectacular early into the second. Lyanco volleying from the edge of the box with a shot which drifted wide of the top-right corner.
Elyounoussi once again proved lively early on, cutting inside from the left before curling a shot towards goal which Rushworth gratefully claimed.
Lincoln’s bright spark continued to be Vernam who seemingly produced a carbon copy of the Norwegian's strike, this one veering off target past the far post.
A triple change was in order on the hour mark; Sam Edozie, Stuart Armstrong and Theo Walcott on for Walker-Peters, Salisu and Adam Armstrong respectively. The hosts reverting to four at the back.
The resulting Saints pressure produced two efforts in quick succession. First Elyounoussi heading just over from inside the six-yard box, before substitute Armstrong grazed the crossbar from range.
Eventually that pressure told. A cross in from Walcott saw Elyounoussi try an overhead kick at the back post. This effort was met by the keeper but fell to Adams inside the six-yard box, who poked home his second.
This proved to be the deciding moment of the game, therefore securing Saints a place in the quarter-finals of the League Cup for the first time since 2017.
Jones’s side return to St Mary’s on Boxing Day, where Brighton visit in the Premier League.