The hosts had plenty of bark, particularly after Morgan Roberts nudged in the opener, but the Pilgrims toughed it out and levelled through Keaton Ward deep into first-half stoppage time to swing the pendulum.
Jimmy Knowles confidently rasped home from the penalty spot just before the hour and United grew in stature, comfortably securing promotion to the National League by sapping the belief of a Brackley side that huffed and puffed without looking like blowing down the house.
Winning boss Ian Culverhouse admitted the end of the opening 45 had caused him concern but said the solid foundations built in penalty shootout wins at Alfreton and Scunthorpe in the previous rounds of the play-offs had stood Boston in good stead.
“I am so proud of the group, they have been magnificent and what a way to do it,” he said.
“When you get the momentum behind you, the two away games, I know we won them on penalties without scoring a goal, but the belief that gave to everyone was fantastic.
“We were hanging on in the first half, they were better than us and asked so many questions so to come through that and get the win speaks volumes.
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