The Pilgrims trailed 1-0 at half-time before conceding a second goal a minute from time.
The result at Bradley FDC sealed a league double for Cleethorpes over the Pilgrims.
Boston (4-4-2): Alex Smith (Harry Payne 46); James Gordon, Daniel Moulds, Calum Stewart, Jaydon Thorbourne; Scott Floyd, Matthew Nezval, Casey Castle, James Daly; Mackenzie Overend (Lewis Millington 60), Sammy Perez (George Hobbins 55).
The Jakemans Stadium York Street Boston Lincolnshire PE21 6JN View with Google Maps
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