Despite a brave effort two games in three days proved too much for us as we bowed out of the William Hill Scottish Cup on Monday night to full time Saints.
There were three changes to the side which had went down at Falkirk with Joe Mbu, Lewis Milne and Dean Brett coming into the starting line.
Colin Cameron dropped himself to the bench while Mark Ramsay was a late withdrawal due to illness and Jamie Stevenson was sidelined with a bruised shin.
Saints opened well and in seven minutes MacKay's curling 20 yard free-kick was deflected past the post by the diving Flynn.
We were hemmed in but in 15 minutes McCracken showed coolness under pressure from Coult to clear up a potentially dangerous situation.
And in 20 minutes McKenzie and Milne had shots blocked as we rallied but at the other end, a minute later, Davidson fired over from the edge of the box. Then in 25 minutes a neat move opened up the Cowden defence and  Scobbie's raking 20 yarder went just over. At the other end, on the half hour, Brett latched onto a loose clearance and his low shot went inches past Mannus' right hand post. Saints went oh so close in 37 minutes when Craig let fly from 19 yards and the ball came back off Flynn's right hand post with the keeper beaten but two minutes later O'Brien sent Miller into the St Johnstone box and his low shot was saved by Mannus and then Milne's 25 yarder produced a fine finger-tip save from the keeper.
As the game opened up, in 42 minutes MacKay's cross was headed strongly by Davidson towards Flynn's bottom left hand corner but the 'keeper made a great save to keep the scoreline blank at the break.
We made a bright start to the second period and O'Brien's header rolled just wide but as Saints retaliated Tade went close.
However, eight minutes into the half the SPL side went ahead when David McCracken managed to fire low into the net after a corner had not been properly cleared. But we immediately retaliated when McKenzie broke into the Saints box and Mannus dived to save his low shot then in 64 minutes the little winger got free again and this time fired inches wide.
But with 14 minutes, to go Saints got the vital second goal. Davidson got free in the Cowden box and as Flynn dived at his feet the midfielder went down and referee Beaton pointed to the spot. It looked a little harsh as it appeared that the keeper had got to the ball first but Steven McLean made no mistake from the spot then with three minutes left the Cowden off-side trap misfired and Gregory Tade ran through for number three to put an unfair reflection on the scoreline.