Boston pulled level in the game and were shaping up as the likely winners when left-back Austin McCann bundled over Lewis Haldane. It was a clear penalty, Rovers' ninth of the season, and the keeper was sent the wrong way by Walker.
The reverse drained Boston who had arrived with two Easter wins behind them and they quickly opened up for Junior Agogo to score Rovers' third with a solo break.
There could easily have been three goals in the first three minutes all from corners.
Craig Disley got in a strong header from Rovers first but it was a fraction too high. Julian Joachim then had a chance for Boston but, wary of a hamstring injury, he failed to stretch fully with the goal at his mercy.
The third chance brought a tremendous save by Conrad Logan from Steve Elliott's header which looked set for the top right-hand corner of the Boston net. Even Elliott went up to congratulate the young Boston keeper on that one.
Loaned from Leicester as an emergency signing following the return of Michel Kuipers to Brighton at the end of his 93-day loan, Logan went on to have a brilliant afternoon and without him Boston's defeat would have been much heavier.
Rovers took the lead after 27 minutes when Agogo drifted to the right where Walker found him with a 15-yard ball. Boston anticipated a run at goal; instead Agogo delivered a perfect cross outside the far post where Disley pounced to head in his eighth goal of the season, a personal best.
It was not a comfortable lead and Boston, who freshened their attack for the second half, were level on 55 minutes. A long cross from the right found sub Brad Maylett heading back across goal where Joachim stooped to nod in his season's 16th.