The Blues looked in trouble when Rob Street struck first for the Imps, but goals by Tyrique George and Facundo Buonanotte completed the comeback.
At Anfield, Isak’s first goal for Liverpool was the headline moment, though Federico Chiesa did the heavy lifting. The Italian created both strikes, for Isak and Hugo Ekitike, in a 2-1 victory.
However, Ekitike is now facing a suspension after being shown a second yellow card for removing his shirt when celebrating his late winner.
Elsewhere, Wolves edged past Everton 1-0 and Brighton swept aside Barnsley 6-0, Diego Gomez hitting a sensational four.
Premier League outfit Burnley were upset by Cardiff, who play in League One, while Fulham squeezed into the next round with a narrow win over Cambridge.
Wrexham eased to a 2-0 victory over Reading, and Wigan beat Wycombe by the same scoreline to round the results off.
More to follow...
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Results
Barnsley 0-6 Brighton
Burnley 1-2 Cardiff
Fulham 1-0 Cambridge
Lincoln 1-2 Chelsea
Wigan 0-2 Wycombe
Wolves 2-0 Everton
Wrexham 2-0 Reading
Liverpool 2-1 Southampton
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