Jon Wilkin put Saints 12-4 up at the break when Chris Riley could not control the slippery ball following the loose forward's grubber kick and Wilkin crashed over.
The challenge of playing Federer clearly galvanises the Briton and he was switched on from the start of Sunday's final, whereas Federer looked distinctly edgy - some loose play handing the Scot a break point in the opening game before another wayward forehand gave up the break.