Two penalties in extra time broke the deadlock in this Northern Premier League President's Cup quarter-final at The Walks on Sunday.
Lynn scored through Nolan Keeley from the spot kick and Witton's Brian Jackson had his effort saved by keeper Mick Drewery.
And that single decider puts Lynn into the semi-final of the competition having held Witton to 1-1 in the first leg.
Both sides looked increasingly leg weary from their games of the previous day and they cancelled each other out.
In a scrappy first half Lynn's best effort was from Keeley with a glancing header he put just wide. By coincidence it was the other penalty taker, Jackson, who could have put Witton ahead on the stroke of half time when he ghosted through and put a header a foot wide of the post.
The effort was there from Lynn but for the most part it was misdirected especially through a low standard of passing. When he ball is given away so often it becomes frustrating for the players and fans alike.
Five minutes into extra time the Witton defence was stretched by Brian Thomson's forceful run down the middle and he was eventually brought down by the sweeper Jay McCombe. Keeley carefully stroked home the penalty.
Keith Rudd had a chance to put Lynn firmly in control when he ran on to Thomson's defence-splitting pass, but Alcock got down to save with one hand.
Well into the second half of extra time, Marty Wiles was judged to have bought down Mick Quinn for Witton's penalty. Jackson did not put much power into the shot and Drewery was able to block it with his legs.
The bookings tally was five - Chris Watts of Lynn and the Witton quartet of Mick Quinn, Ian Hodge, Dave Kelly and Mark Fielding.
Lynn: Drewery, Thompson, Watts, Bircumshaw, Wiles, Thomson, Keeley, Elliott (sub Easthall 78 minutes) Burrows, Rudd, Chapman.
Witton: Alcock, Fielding, Johnston, McCombe Kilduff, Kelly, Jackson, Quinn, Hodge, Salmon (sub Williams 109), Keys.