Lawrie Dudfield was the injury-time hero as his 94th-minute strike won a full-blooded derby for Boston.
The Pilgrims forward ended Lincoln's 12-match unbeaten run after both sides had enjoyed one half of dominance.
Julian Joachim stabbed Boston ahead after Dudfield had shot against the underside of the crossbar before Marvin Robinson fired a spectacular equaliser.
But Boston staged a late rally and, after Danny Thomas and Joachim had been denied, Dudfield lashed home.
Boston Utd: Kuipers, Canoville, McCann, White, Clarke, Silk,
Holland (Thomas 87), Talbot, Till, Dudfield (Hall 90), Joachim.
Subs Not Used: Maylett, McSporran, Melton.
Booked: Talbot.
Goals: Joachim 26, Dudfield 90.
Lincoln City: Marriott, Cryan, McCombe, Brown, Mayo,
Steve Robinson (Frecklington 46), Kerr, Beevers,
Birch (Gritton 85), Yeo (Marvin Robinson 64), Green.
Subs Not Used: Stirling, Wilkinson.
Goals: Marvin Robinson 66.
Att: 4,476.
Ref: K Hill (Hertfordshire).