Todd scored with just ten seconds to spare after Andy Marriott had pushed out a Paul Mullin shot into his path. It was elation for the home fans but a disaster for United, who felt that Todd was offside and protested to the referee at the end.
It was a lively finish in what was a game of few chances.
Gary Roberts gave Accrington the lead on 11 minutes when he dispossessed defender Mark Albrighton at the edge of the area and finished well to make it six goals for the season.
Accrington had more half-chances with Ian Craney ballooning an effort over and Todd, after a neat one-two with Sean Doherty, raced down the wing but couldn't finish.
Stanley were creating the better chances but couldn't get the all-important second against Boston, who have the leakiest defence in League Two.
Boston didn't have a shot in the first half but came out all guns blazing after the break. They got their reward on 49 minutes when David Farrell took the ball past Peter Cavanagh and finished well for the equaliser.
Stanley were passing the ball around well but couldn't make an impact in front of goal as John Coleman put on substitute Andy Mangan for the final 20 minutes.
Boston still had the better chances with Anthony Elding having a close-range effort cleared off the line by Romauld Boco.
They looked like they would leave the Fraser Eagle Stadium with a point but then Stanley launched one last attack.
Mangan hit the upright with a fierce strike and then, as the ball bobbled around the area, Todd got the final touch to give his side the three points.
It prepares them nicely for their huge Carling Cup clash against Premier side Watford on Tuesday night.