Linnets manager Tommy Taylor criticised his side after they made hard work of completing a league double over the Ducks and denting their promotion hopes.
The Walks outfit should have been out of sight before the interval, but it took a special free-kick from Mark Angel after the interval to separate the sides over the 90 minutes.
A frustrated Taylor said: "We dropped off far too deeply in the second half and that's why we picked up so many knocks.
"The players have to realise that they have to perform for 90 minutes, not just 45. That has been our problem of late.
"I thought that our display in the first half was excellent but we ended up making hard work of it and the final winning margin should have been far greater."
Taylor was particularly angry with substitutes Ludovic Quistin and David Staff, who were unhappy about starting the game on the bench.
"Ludovic and Staffy got the hump because they didn't start," fumed Taylor.
"If they don't like it they can go. I pick the team to win matches and players have to accept that.
"I will not be held to ransom by anyone. If players don't like it then they can go down the road."
To mark his 100th league appearance, Taylor installed Jack Defty as captain and the midfielder limped off late in the game to a resounding reception from the 788-strong crowd.
Steve Wilson was back in between the posts, while Gary Setchell returned at left back and Matt O'Halloran replaced Stephen Harvey at right back.
A poor Aylesbury side only managed one shot on target in the whole game and it once again highlighted what a wide-open and winnable league the Southern Premier Division was this season.
Lynn swarmed forward early on, an Angel centre was just missed by Danny Bloomfield and Defty between them while O'Halloran's cross was turned into the side netting by Bloomfield.
Half chances were then wasted by Sam McMahon and Setchell before Angel's free-kick was superbly turned round by visiting keeper Jack Rashid.
On the stroke of the interval Bloomfield tore down the left after receiving the ball from Setchell, but Angel fluffed his lines in front of the target.
Five minutes into the second period Angel stepped up to curl home a free-kick and give Lynn the advantage their first-half pressure had deserved.
But as so often this season - and one of the main reasons for inconsistent Lynn's failure to make the play-offs – The Walks outfit decided to step off the gas and give Aylesbury hope.
A last-gasp Setchell challenge denied Gavin Jaggard a certain equaliser in the 73rd minute, before, two minutes later, Bloomfield failed to gobble up a howler by Liam Folds and Rashid saved well.
Lynn: Wilson, O'Halloran (Staff 59), Setchell, Clark, Hammond, Camm, Defty (Quistin 90), McMahon, Hay (Harvey 90), Bloomfield, Angel.
Unused sub: Higgs.
Booked: Staff, Hammond.
Aylesbury: Rashid, Williams (Edgworth 54), Mead, French (Baker 80), Hayward, Fold, Kearns, Lamb, Doherty, Roberts (Lazarus 85), Jaggard.
Unused subs: Cook, Hodges.
Booked: Williams, Hayward, Fold, Lamb.
Referee: M R Swift (Grimsby). Attendance: 788.