The Armenian minnows, who were reduced to 10 men in the second half, struck twice at McDiarmid Park to secure a 2-2 aggregate draw and book their place in the second round of qualification.
A scrappy opening period to the game suited the visitors more than their opponents, sitting on a one-goal advantage from the first leg, with three bookings inside the opening quarter of the contest proving a sign of things to come.
The Saints really began to up things as the first half wore on, though, coming close to finding an all-important opener on the night through both Scott Brown and Christopher Kane, neither of whom could quite direct their efforts home.
Michael O'Halloran finally provided the home supporters with the moment they had been waiting for on 38 minutes, when angling the ball into the back of the net to level things up.
It was the Armenian visitors who ended the opening 45 minutes the stronger, but still Tommy Wright's men pushed on in search of a second goal as Kane tried his luck from 20 yards out.
A turning point in the game appeared to arrive shortly after the hour mark when Karen Muradyan was shown his marching orders, but seconds later Sekou Fofano squandered his side's best opening to give St Johnstone a real let-off.
Requiring two goals in the remaining 16 minutes, the Scottish outfit needed to find a quick response, and while Brad McKay did pull one back late on with a well-taken strike inside the box, it was not to be in the end.