HEADERS in each half from Joe Francis and Jack Defty secured the win, with manager Keith Webb reserving special praise for Defty.
Defty got his first goal since November 27 - which was also the last time The Walks outfit got a clean sheet.
Webb, who also lauded groundsman Maurice Bunting for his work on the pitch after a deluge of overnight rain, said: "I'm really pleased for Jack Defty, I was desperate for the lad to score, and he hit the bar twice.
"It was a good goal - good build-up, cross and header, and it was a big weight off his shoulders.
"The way the players appreciated it - everyone ran over to him. They appreciated the work that he does.
"I'm delighted for him and delighted with the team.
"I haven't seen too many faults with the side, and I'll defy anyone who has."
Prior to kick off on Saturday a minute's silence was observed for former chairman Brian Rawlinson, who passed away shortly before Christmas.
It looked like Defty's drought would continue on 14 minutes when his looping header from Francis' corner hit the bar.
In an intense first quarter-hour, Mark Camm and Defty fired over, while Rugby's David Pearson was also off target shortly afterwards.
Before Lynn had time to regret these chances, in the 25th minute they went ahead when Steve Melton's cross from the right beat everyone except Francis at the far post, who nodded past the stranded keeper Ross Faulds.
The sides traded yellow cards as referee Ross clamped down on sliding tackles which were inevitable on a muddy pitch.
Lynn came out buzzing in the second half, Danny Bloomfield's effort deflected for a corner and Faulds somehow diving to deny Defty and Melton at his near post.
Defty was also unlucky as his bicycle kick when set up by brother Charlie smacked the bar.
Just before the hour mark Rugby's Tom Breward was sent off when he picked up a second yellow for a two-footed tackle on Francis.
At last Lynn's pressure told on 64 minutes when a good move down the left ended with Francis' superb cross directed home by the stooping Defty for his 70th goal for the club.
Former Linnet Dave Staff exited the game to generous applause, but it was no first-time win for new Rugby boss Rod Brown and assistant manager Paul Devlin.
Francis and Dean West had further chances as Lynn closed in on a deserved victory to stay top of the league.
Lynn: Howie, West, Chapman, C. Defty, Crane, Camm (Fisk 79), Melton (Turner 61), Sedgemore, J. Defty, Bloomfield (Nolan 72), Francis. Subs not used: Fleming, Murray. Booked: Francis 34, Crane 36.
Rugby: Faulds, Stringfellow, Morley, Herbert, Gordon, Breward, Devlin (Evans 61), Musgrove (Francis 71), Pearson, Stone, Staff (Kolodynski 75). Not used: Edge, Aladetoun. Booked: Devlin 9, Musgrove 45, Breward 52, 58. Sent off: Breward.
Referee: S. Ross (Boston); Attendance: 1,025; MoM: Jack Defty.
Stats, Lynn first: shots on target 6, 1; off target 7, 1; corners 6, 5; offside 1, 4; free-kicks conceded 11, 14.