Lynn's two summer signings Chris Watts and Roy McManus scored the goals which held Clapton on Saturday.
They we on target in the first half of an exciting FA trophy First Qualifying Round tie.
Watts shot Lynn into a 15th minute lead from 20 yards being given far too much room by Clapton from a short free-kick supplied by McManus. Watts had time to steady himself and then clip in a shot which was always beating keeper Ron Lee and went high into the top corner of the net.
When McManus knocked in his goal a minute before half time it was to bring Lynn level after a two goal burst by Clapton.
A flowing move involved Lindsay neatly heading on into the path of Benefer who was making ground on the unguarded right wing. Without hesitation Benefer swung in a centre which brought confusion to Clapton with the keeper and a defender neither managing to clear the ball.
McManus was there to settle the matter with careful side-foot into the net.
These goals came in a half when Lynn promised quite a lot, but achieved little. In fact it was a classic example of team poaching two goals from two raids.
Clapton were a better side attacking than defending and had twice gone close through Dormer and Gormley before Watts scored. Gormley, tall and hefty, was to have a rare tussle throughout this match with Mick Wright and it is not biased reporting to say that the Lynn skipper came out on top especially as the game progressed.
It was a tragedy that Wright's one error should lead to a goal for Clapton in the 30th minute his intended pass out of defence went straight to Gormley and with Lynn caught off balance Gormley beat Wilson and his pass across to Dormer left the winger with only Thompson to beat.
In two previous similar situations Thompson had blocked him but this time Dormer steered his shot home.
In the 34th minute it was Dormer again with a diving header from a cross by Wise which put Clapton in front. Although the linesman had indicated an offside during the attack the referee overruled him.
Instead of letting this get them down, Lynn replied through McManus just before the interval, which set them up for a second half where the goals dried up but the entertainment certainly didn't.
For lengthy periods Lynn looked the more organised and controlled side, especially in mid-field where the contributions of Watts, Goose and Benefer were important. Goose made some telling runs at the Clapton defence, once linking well with Lindsay - who was showing all the little flicks and knock-ons of the Lindsay of old - before being crowded out in the penalty area.
Rudd had the goal in his sights on two occasions, the first with a mis-hit shot which Lee saved and then in the 72nd minute a powerful header from a cross by Goose which went inches over the top. Lindsay was just as close when from the narrowest of angles he turned and swung in a shot which hit the side netting.
In the 80th minute a move involving Rudd and Lindsay so nearly brought a winner. The cross by Rudd was left by Watts for McManus who lifted in a shot which was palmed away by the keeper.
In the final seconds of the game it was Lynn's turn to defend and when a rebound put Dave Wise clear, Thompson spread himself to block the shot. The Lynn keeper also went down by the post to save from Rogers.
Lynn: Thompson, Rider, Wilson, Wright, Johnston, Watts, Goose, Benefer, McManus, Lindsay, Rudd, sub Barrett.
Clapton: Lee, Dring, Faldo, Shirley, Taylor, Wise, Shorey, McPherson, Gormley, Pace, (Rogers 73 minutes), Dormer.
Referee: A Nathan (Chadwell Heath)