Lewis Hilliard and Joe Robinson had fired United into a 2-0 lead in Warwickshire, but Kelvin Langmead soon cut the deficit.
It appeared to be United's afternoon when Dion-Curtis Henry denied David Morgan from the penalty spot, but Jordan Nicholson had the last word with a thunderbolt of an equaliser in stoppage time.
United had the better of the opening stages, with Hilliard lifting an effort off target while Connor Anderson blocked well to deny Waide Fairhurst.
Henry was alert to turn aside Morgan’s drive midway through the first half but United went in front after 32 minutes when Fairhurst laid the ball off for HILLIARD to crash an unstoppable effort beyond the reach of ex-Pilgrim Christian Dibble.
Dibble subsequently saved well to deny Hilliard a quickfire second before Robinson lifted the ball over from close-range after the returning Nat Brown had nodded down a corner delivery.
Boston started the second half well too and Callum Chippendale had an effort deflected wide before two Hilliard attempts from distance nestled narrowly wide.
Langmead glanced a header wide following Greg Tempest’s deep corner but United were soon two goals to the good, on the hour mark, when ROBINSON powered home Hilliard’s delightful ball from the left.
United’s two-goal cushion lasted only seven minutes with LANGMEAD ghosting in to power home a header on the end of Tempest’s corner.
Town were now well in the ascendancy and were awarded a spot-kick for Courtney Wildin’s foul on James Clifton. Henry rescued his team-mate though by saving Morgan’s firm penalty.
Nuneaton had further efforts on goal through substitutes Joe Ironside and Iwan Cartwright, while David Moli heade wide from a corner.
United appeared to be home and dry but a minute into stoppage time they failed to close down NICHOLSON, who lashed home a beauty from just outside the box and dash Boston’s hopes of a second away win of the campaign.
Nuneaton (4-1-2-1-2): Christian Dibble; James Clifton, Kelvin Langmead, Connor Anderson, Luke Higham (Iwan Cartwright 65); David Morgan; Billy Daniels (Joe Ironside 65), Greg Tempest; Jordan Nicholson; David Moli, Aaron Williams. Subs (not used): Tom Elliott, Dan Demkiv, Tommy Wright.
Boston (4-4-2): Dion-Curtis Henry; Ben Gordon, Joe Robinson, Nat Brown, Courtney Wildin; Marcus Marshall, Callum Chippendale, Lewis Hilliard, Jason St Juste; Jay Rollins, Waide Fairhurst (Cameron Johnson 72). Subs (not used): Liam Adams, Lamin Colley, George Couzens, Michael Emery (gk).
Referee: Matthew Donohue.
Attendance: 577.