McGowan, recalled to the starting line-up after being left out in midweek, headed in Jereon Tesselaar's excellent cross from the left on the half-hour and added the second from the penalty spot a minute before half-time after Zoenek Kroca was harshly penalised for handling in the box.
Killie had enjoyed the better of the play in the early stages and Craig Samson had to make fine saves from Paul Heffernan in the first half and Manuel Pascali in the second.
Kroca headed against the bar twice late in the second half but Hasselbaink wrapped up all three points with a neat header at the back post with five minutes remaining.
St Mirren had not scored in their three previous home league games and manager Danny Lennon made just one change from the side that beat St Johnstone in the Scottish Communities League Cup on Tuesday, with McGowan replacing Hasselbaink up front.
Both sides had been praised for their free-flowing football in the opening weeks of the season and both were keen to build patiently from the back in the early stages.
Kilmarnock were first to threaten after one of those fine passing moves as Gary Hay slipped the ball through for the in-form Heffernan but his shot on the turn was well parried by Samson.
Cammy Bell was called into action for the first time after 15 minutes when Steven Thompson's downward header was tipped round the post by the Kilmarnock goalkeeper.
The hosts then went ahead against the run of play on 32 minutes when Tesselaar's excellent cross from the left was headed across Bell and into the far corner by McGowan for his first goal of the season.
Having got the goal, St Mirren grew in confidence and Thompson just failed to get on the end of another fine cross by Tesselaar before Gary Teale had claims for a penalty waved away.
The home side were awarded a penalty just on half-time, though, as Steven Thomson's cross struck Kroca's arm inside the box. Referee Stephen Finnie originally turned away the claims but reversed his decision on advice from his assistant and McGowan stepped up to slot home his second goal of the afternoon.
St Mirren nearly added to their lead within five minutes of the second period as McGowan released Teale down the left and his cross was just out of the reach of the on-rushing Thomson.
McGowan was at the heart of everything the hosts did going forward and more neat skills from the former Celtic striker created space for the cross where he found Thompson in the box and his header was brilliantly saved by Bell.
Killie boss Kenny Shiels brought on David Silva and James Dayton in an attempt to get back into the game and moments later Manuel Pascali's long-range drive forced Samson into a fine save.
McGowan nearly had his hat-trick on two occasions, firstly with a wonderful chipped effort 10 minutes from time but the ball crept inches over the bar before another right-footed effort flew just wide of Bell's right-hand post.
Kroca headed against the bar from a corner but St Mirren wrapped up all three points with five minutes to go as Hasselbaink headed in at the back post from David Van Zanten's cross.
Kilmarnock went close again to a consolation goal but another Kroca header crashed off the bar before the hosts wasted a great opportunity for a fourth as Teale opted to pass to Hasselbaink when through on goal but the Dutch striker was in an offside position.
Bell made one final save from Thomson's header in stoppage time as St Mirren cruised to their first league victory in four games.