Saints started the better side with former Airdrie man Willie McLaren firing in a couple of long-range efforts, the second of which Graeme Smith did well to parry.
It was no surprise when they took the lead in the 21st minute with McLaren involved again. This time he skinned Danny Murphy on the right and sent a perfect cross for Peter McDonald to scoop the ball over Smith and in off the underside of the bar.
As the half wore on it was still Saints who looked most likely to score. First it was a Jason Scotland header that sailed over when the striker was under no pressure.
Then Smith had to react saving full length from a Martin Hardie header which was heading for his bottom corner.
Saints then took a grip of the second half and it was again no real surprise when they scored a second. Smith had initially done well to keep out Hardie's long-range effort but he was helpless when Goran Stanic hit the byline and crossed for Scotland to head home from close range.
It could've been worse for Well only minutes later when Smith was forced to make two more saves, first from Paul Sheerin and then from Kevin James' downward header.
Motherwell almost gifted Saints a third when Smith drove the ball off his own defender Stephen Craigan, the ball fell for McDonald but Smith recovered to save.
With seven minutes left Motherwell pulled one back when Ross McCormack toe-poked home a Scott McDonald cross from close range. Kevin Cuthbert then did well to hold on to a McCormack drive with David Clarkson and McDonald waiting to pounce.
Saints finished their fifth game against an SPL side unbeaten this season and move to their second semi-final of the campaign.