And it ensured that the sides will meet again in Paisley on 18 March.
Former Chelsea midfielder Jody Morris had been handed his first start for St Johnstone, who are aiming for their second semi-final spot in a row, after scoring last weekend.
Steven Anderson and Craig returned from suspension, with Rocco Quinn and Paul Sheerin dropped to the bench, while Sean Lynch was not named in the squad.
Stewart Kean made way for fit-again Craig Dargo in St Mirren's front line after last week's defeat by Kilmarnock.
And the Scottish Premier League outfit looked fairly comfortable as the two sides sussed one another out during a quiet opening spell bereft of the kind of skilful play synonymous with watching Fifa president Michel Platini.
Buddies defender David van Zanten sent a 22-yard drive a few yards past the home post.
But St Johnstone responded by taking the lead after 32 minutes.
Murray felled Stanic as the left-back burst into the penalty box.
And Craig sent goalkeeper Graeme Smith the wrong way from the spot.
Liam Craig put St Johnstone ahead in Perth
St Mirren were knocked out of their stride and were under siege for the remainder of the first half.
But Peter MacDonald squandered the best chance of a second goal, firing straight at Smith after making space for himself on the edge of the box.
St Mirren came back into the game after the break and Mark Corcoran used the wind to send a corner kick curling towards goal but off the top of the crossbar.
MacDonald was again the main threat for the home side, a low drive from 20 yards trundling a few feet wide of the post.
St Johnstone survived some intense pressure before threatening again at the other end, where Van Zanten cleared a Jackson header off his own goalline and Saints were denied a couple of penalty claims.
Main had yet to be tested but found himself picking the ball out of the net after 73 minutes.
Dorman latched on to Dargo's head flick before prodding the ball over the goalkeeper's head and into the unguarded net.
Smith made a double save from Kevin James and Andy Jackson in the closing minutes to deny St Johnstone a winner.
St Johnstone: Main, Irvine, Stanic, Anderson (James 86), Rutkiewicz, McManus, Morris, Craig, Jackson, Milne, MacDonald (Sheerin 79). Subs Not Used: Quinn, Wilson, Cuthbert.
Booked: Anderson, McManus.
Goals: Craig 32 pen.
St Mirren: Smith, van Zanten, Maxwell (Kean 72), Haining, Potter, Murray (McGinn 45), Dorman, Mason, Corcoran (Miranda 88), Dargo, Mehmet. Subs Not Used: McAusland, Howard.
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