Goals from Stewart Talbot, Lee Canoville and Paul Ellender outweighed a single reply from Jonathan Parkin.
Macclesfield started the brighter of the sides with Parkin and Clyde Wijnhard posing plenty of problems to the home rearguard, the former going closest with a rising drive in the 11th minute.
However it was Boston who took the lead on 15 minutes when earlier substitute Asa Hall and David Galbraith linked to set up Talbot and his 18-yard angled drive looped over keeper Alan Fettis via a deflection off David Morley.
Macclesfield went close to drawing level in the 24th minute when Danny Whitaker wriggled into the area but saw a 12-yard shot hit on to the bar my home keeper Conrad Logan.
Boston answered with low strikes by Lawrie, Dudfield and Galbraith but each time Fettis saved well.
Fettis, though, was out of luck in the 32nd minute when he managed to parry a fierce angled drive by Canoville only for the ball to spin back over the line for a 2-0 Boston lead.
The second half was only two minutes old when Macclesfield halved the deficit, Parkin netting with a diving ten-yard header from Kevin Sandwith's corner.
The 57th minute almost brought an away equalizer when Whitaker again got into a shooting position, but his fierce low effort was well saved by Logan.
Macclesfield threatened again in the 67th minute when Parkin got on the end of a Paul Harsley flag-kick but his header flew straight at Logan.
The visitors produced some excellent passing work and frequently had the home defence at full stretch.
Boston's attacking work was less evident, although in the 70th minute Dudfield broke clear but shot at Fettis. And moments later Julian Joachim headed inches wide from a Galbraith corner.
Boston sealed victory in the 81st minute when Ellender showed great finishing technique when flicking in at the near post from another Galbraith corner.