Without a win or a goal in their previous two SPL fixtures, Caley Thistle knew the importance of a good start and Cowie provided it with only six minutes played.
In easily the best move of the opening 45 minutes, Dennis Wyness laid the ball out to Barry Wilson, who in turn played in Roy McBain and his cut back was promptly dispatched from 12 yards by the unmarked Cowie for his fourth goal of the season.
Heavy winds and rain curtailed any hopes of a free-flowing encounter and as a consequence there were few chances in the first half.
The best of the opportunities, however, came for the hosts with Cowie firing wildly over from virtually the same position he scored his goal after being set up by David Proctor.
Russell Duncan was then presented with a sight of goal from McBain's cross, but even though his goalbound shot appeared to be deflected wide by Will Haining, referee Crawford Allan decided to award a goal kick.
Playing with the wind at their backs in the second half, St Mirren offered more of a threat in the final third with Stewart Kean forcing Michael Fraser into his first real save early on.
The visitors almost shot themselves in the foot when David van Zanten gave the ball away to Wyness, but Caley Thistle's top scorer could only curl his effort straight into the hands of Chris Smith.
Inverness also rode their own luck with a free-kick from Mark Corcoran forcing McGuire to head the ball onto the upright before it bounced away to safety.
St Mirren's best opportunity for an equaliser fell to their most dangerous player Kean as he charged through the Caley Thistle reaguard, but with a clear sight of goal, he could only divert his shot wide of a relieved Fraser's right-hand post.
Still the Paisley side would not concede and Gary Mason was only inches away from levelling proceedings with a clever volley that looped agonisingly wide.
A second yellow card for Haining, however, 14 minutes from time all but ended the visitors' hopes of a point as Caley Thistle comfortably saw out the rest of the match to secure the victory.