The Pilgrims got the better of their mid-table opponents to at least ease their worries at the basement end of the division - a result that also ended the Bees' four-match winning run.
The game was just eight minutes old when Boston broke the deadlock. Makeshift left-back David Galbraith found space down the flank and delivered a cross for Mark Greaves to head in from six yards.
But three minutes later Barnet drew level when Adam Birchall forced his way down the right and cut the ball back for Richard Graham to fire in from inside the six-yard box.
Boston pressed again and, in the 19th minute, another Galbraith centre found Greaves once more. But this time he saw his shot blocked by Simon King. Then, moments later following another good home build-up, Francis Green contrived to shoot wide from six yards with only keeper Ross Flitney to beat.
At the other end, in the 24th minute, Barnet moved back on to the offensive and a long-range shot by Barry Cogan crashed away off the top of the home crossbar.
And the visitors went close again in the 37th minute when Birchall wriggled into space and his low shot was well blocked by home keeper Andy Marriott.
Boston hit back again just before the break when Chris Holland crossed from the left. Green swung and missed and then Brad Maylett fired into the side-netting.
The second half was only 60 seconds old when Boston regained the lead. Drewe Broughton nodded down a Galbraith cross and David Rowson raced through to deliver a cross-shot that Ismail Yakubu unluckily diverted into his own net.
For a spell after that Barnet sought to hit back again and they played a lot of neat football but without being able to conjure up a clear opportunity.
The next clear chance in fact went Boston's way when, following a Galbraith corner, Ian Miller headed inches wide. Then, on 74 minutes, Green saw a long-range shot well held by visiting keeper Flitney.
Boston continued to battle well and withstood some further Barnet pressure. But the final chance fell the home side's way when Dany N'Guessan's low drive was saved by Flitney.