This game lived up to the previous meetings with only one goal between the sides which was enough to earn Saints a quarter-final tie at home to Celtic.
The opening stages saw the home side take the game to Motherwell as they looked to find the opening goal. All they had to show for their possession was a snatched shot over the crossbar by Hugh Murray.
After 20 minutes Well slowly found their way into the game. Home keeper Chris Smith was a little lucky when he stumbled going for a Marc Fitzpatrick shot but he reacted well to save. The only other real chance of the opening period fell to Well's Jim O'Brien but his effort was blocked by Jack Ross.
As the players trooped off at half-time many in the stadium were already thinking ahead to a penalty shootout given the lack of firepower on display.
The start of the second period was much livelier with Saints being denied twice in the opening ten minutes. Dennis Wyness looked to have been sent clear by a Billy Mehmet flick, but Mark Reynolds reacted quickly to clear.
Minutes later Mehmet released Ross on the right and the full-back's blistering 25-yard shot was beaten out by Graeme Smith.
Saints continued to press and Andy Dorman was quick to pounce on a weak Paul Quinn clearance, but Mehmet could only volley his cross wide from close range.
The play switched to the other end and Well came close through Fitzpatrick and Stephen Hughes, with the midfielder shooting over on a couple of occasions.
The visitors were punished for these misses with only five minutes to go when Saints took the lead. Sub Craig Dargo sent Mehmet clear of the offside trap and the striker slammed his shot low past Graeme Smith.
This was enough to seal the tie and see Saints move into the quarter-finals with a first win at their new stadium.