Two goals in the final minute gave Boston their fifth away victory whilst depriving Orient of the point they needed to guarantee Third Division survival.
Victorious manager Steve Evans said: "We stepped up from third gear into fourth during the second half and started to control the game. It wasn't pretty stuff but we deserved our win." Meanwhile beleaguered O's Manager Martin Ling reflected: "I thought we'd get the point we needed when Andy Scott scored but then we threw it away like only we can.
"Things are getting worse, we still need a point but frankly I can't see where it's coming from." A desperate game came to life on 67 minutes when the Pilgrims Lee Beevers left a corner from Danny Thomas to fire the ball home from close range after goalkeeper Glenn Morris had failed to collect the ball cleanly.
However the O's appeared to have salvaged their lifeline point when Scott blasted the equaliser following a Matthew Lockwood free-kick that visiting keeper Paul Bastock under pressure from Chris Tate failed to hold.
However, the visitors responded immediately and within four minutes had regained the lead. Tate, who was still recovering from his earlier clash, pulled up quickly as he moved to a clearance allowing Ben Chapman to intercept.
He released the impressive Thomas down the left who squared the ball for David Noble to score with ease.
Then in the dying seconds, sub Lee Thompson settled the issue shooting home from close range after Noble had broken quickly down the right to exploit a stretched home defence.
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