Lowery earned PGA Tour membership through 1987 PGA Tour Qualifying School. His best season on the PGA Tour was in 1994, when he finished 12th on the money list and won his first tournament.
He played one of the most memorable stretches in PGA Tour history at The International in 2002. The event was played under the Stableford Points format. On the 14th hole, Lowery went up and down from the water on a "splash" shot, leading to a birdie earning two points. On the following hole, he holed out a wedge from the fairway for an eagle earning five points. Two holes later, on the par-5 17th, Lowery holed out a shot from over 200 yards for a rare double eagle (or albatross) to earn eight more points and suddenly pull within one point. His double eagle was one of the most dramatic in PGA Tour history since Gene Sarazen's at the 1935 Masters Tournament. Lowery ultimately lost by the same margin after missing a birdie putt on the last hole.[2]
Lowery missed most of 2007 with a wrist injury. The PGA Tour granted him a partial exemption for the 2008 season. He needed to win more than $250,000 during his first eight starts in 2008 in order to re-gain his full exemption on the PGA Tour, but that became a moot point when he won the 2008 AT&T Pebble Beach National Pro-Am. The victory gave him a full two-year exemption.