Goals from Mark Surgenor, Neal Gawley and Matthew Tipton ensured that Ballymena clinched their first-ever Premiership victory at Ferney Park.
Surgenor scored the Sky Blues' first league goal at the County Fermanagh ground with a 25-yard shot off the underside of the bar on four minutes.
Liam Martin levelled with a low shot on 40 minutes but Gawley found the net with a curling 20-yard free-kick on 69.
Tipton made it 3-1 with a well-executed right-foot finish in added time.
Johnny Lafferty dragged a shot wide of the post, before Surgenor put the visitors in front with his spectacular effort.
David Cushley went close with two good efforts but Martin equalised when he swivelled in the box and drove low into the corner from 12 yards out after meeting Jason McCartney's corner.
Lafferty fired a left-foot free-kick wide of the post but Gawley beat Stefan McCusker with a well-taken 69th-minute free-kick, and Tipton made the points safe.