Haas, bidding for his third win of the season, shot a 31 on the back nine and finished at 4-under 67 for a 10-under 132 total. David Edwards (68) was second.
Senior PGA Championship winner Denis Watson (67) was 6 under, and Brad Bryant (65) and Mark James (70) were 5 under.
Haas led by one shot after the first round, then fell behind Edwards with a double bogey on the eighth hole. But Haas, the only player on the senior circuit with multiple wins this year, picked up strokes on six of the next seven holes -- a stretch highlighted by two straight brilliant shots -- and held the lead the rest of the day.
Haas holed a 44-foot birdie putt on No. 13, then placed his tee shot on the par-3 14th on the elevated back edge of the green. The ball sat on the fringe before rolling within 4 feet of the cup. Haas putted for birdie to move a stroke ahead of Edwards.
Edwards won the 3M Championship in Minnesota last August, but this season has been a major struggle. Three straight birdies gave Edwards, currently 58th on the money list, a two-stroke lead through 11 holes, but he could only make pars while Haas was stringing together birdies.
Edwards' second shot on the par-4 17th found the water, though he got up-and-down from 80 yards for bogey.
Watson finished with seven birdies and three bogeys.
Bryant shook off a rough first round by shooting the low score of the day. Bryant made six birdies, including one at No. 18, which he bogeyed Friday.
Jay Sigel, Morris Hatalsky and Dave Eichelberger were 4 under, and Hale Irwin topped a group at 3 under.
Jim Thorpe, the winner at Glen Oaks Country Club in 2001, was in the mix for much of the day before imploding down the stretch. Thorpe triple-bogeyed 17 and bogeyed 18 for a 73 and 2-under total.