Lynn's new goal-scoring combination of Chris Watts and Roy McManus struck again in Wednesday's FA Trophy replay at The Walks.
They scored vital second half goals against Clapton which opened the way for victory. This followed Saturday's first round tie which ended in a 2-2 draw when they were Lynn's scorers.
Clapton's defensive failing which were apparent on Saturday soon showed up in an exciting first half. There were several suicidal passes back to keeper Lee who also saved well from Lindsay.
But Clapton attacked with some menace and Shorey thundered in a shot from all of 30 yards which left a mark on the post. Still a goal would not come, even when Rudd turned in a shot which hit Lee when he appeared to be going in the wrong direction.
The second half may have lacked in finesse, yet made up for that with all the goals. Chris Watts got the first in the 47th minute, his shot going just inside the post after Rudd's back header had put the defence off balance.
Clapton then had their best period of the match and from a corner hit low into the goalmouth Taylor got the touch which turned the ball over the line. This was in the 53rd minute and shortly after Rogers had a shot rebounding off the post and Gormley slid the ball into the side netting after getting round Thompson.
Lynn had been struggling but McManus lifted them with a fine goal, curling a low measured shot into the corner of the net in the 72nd minute. Rudd finally settled it in the last minute when two defenders hesitated fatally and he swept through to tuck away his shot.
Lynn: Thompson, Rider, Johnston, Wilson, Wright, Watts, Goose, Benefer, McManus, Lindsay, Rudd, sub Wiles.
Clapton: Lee, Dring, Faldo, Shirley, Taylor (sub Cleaver 60), Wise, Shorey, Rogers, Gormley, Pace, Staines.