A new stadium record crowd of 2,694 watched on as the Pilgrims suffered defeat at the hands of the Linnets, despite a decent showing from the home side.
Substitute Gold Omotayo opened the scoring in the 75th minute and Olly Scott capped the win with a second for Lynn in stoppage time.
United should have taken a seventh minute lead when Scott Pollock forced his way through - only to drag his shot across goal and wide of the far post.
Lynn went close when Josh Barrett rattled the crossbar with a 20-yard free-kick, while Sheffield United loanee Joe Starbuck fired an effort off target for the Pilgrims after seeing his first drive blocked.
The first real save of the match was made by Sam Long at the start of the second half, denying Barrett, while Jordon Crawford saw a low drive gathered by Paul Jones at the other end.
Sam McLintock rattled the crossbar from 20 yards in the 63rd minute, with Crawford unable to turn home the rebound.
The visitors took the lead 12 minutes later when Barrett crossed from the right and OMOTAYO got in front of substitute Jo Cummings to steer the ball home from close-range.
The away side wrapped up the points in the first minute of stoppage time when SCOTT beat Long at his near post with a firm drive after Lynn had broken sharply on the Pilgrims, who were pushing strongly for a leveller.
Boston (3-4-1-2): Sam Long; Zak Mills (Jo Cummings 73), Shaun Pearson, Ben Pollock (Harry Lewis 80); Joe Starbuck, Tom Platt, Sam McLintock, Keenan Ferguson; Scott Pollock; Jordan Burrow (Jake Wright 73), Jordon Crawford. Subs (not used): Will Atkinson, Tom Solanke.
King's Lynn (4-2-3-1): Paul Jones; Aaron Jones, Kyle Callan-McFadden, Josh Coulson, Tyler Denton; Michael Clunan, Theo Widdrington (Christian Oxlade-Chamberlain 62); Ben Stephens (Gold Omotayo 69), Josh Barrett (Adam Crowther 78), Olly Scott; Ken Charles. Subs (not used): Zain Walker, Sam Blair (gk).
Referee: James Westgate.
Attendance: 2,694 (482 visitors).