After taking a first minute lead through centre-back Richard Hope, Shrewsbury looked destined to recall their fifth home win of the campaign as the game entered into its closing stages - particularly as the visitors were down to 10 men following the 64th minute dismissal of Simon Rusk.
But, with their first and only shot on target, substitute Noel Whelan snatched an 88th minute point for Boston when he netted at close range.
After conceding a last minute leveller at top of the table Wycombe in midweek, which was to cost them victory, Boston found themselves behind after just 90 seconds at Gay Meadow.
Kevin Sharp, recalled to the Shrews team after their 3-1 win over Darlington on Tuesday, curled in a free- kick that Hope nodded against the bar - but he reacted first to the rebound and hooked the ball home from five yards.
As the half unfolded, Boston recovered from their early setback to earn a large share of possession, but only had long range efforts from Rusk and skipper Paul Ellender to show for their efforts.
After the break, Francis Green fired just wide of the Shrewsbury goal, but their task was made even harder on 64 minutes when midfield man Rusk was ordered off for a second bookable offence.
Neil Sorvel and teenage midfielder David Edwards both went close to securing victory for Shrewsbury in the last 10 minutes - but with 90 seconds remaining Whelan was on hand to convert a Green cross to earn his side an unlikely point consigning Shrewsbury to their fifth home draw of the season.