The 52-year-old Maggert parred the final three holes after making eight birdies and a bogey on the first 15 at Canyon Meadows. The three-time PGA Tour winner has five victories on the 50-and-over tour. He won four times last year, the first two majors in the Regions Tradition and U.S. Senior Open.
''I came in here a little bit kind of angry and a little bit more hungry because of the way I played this year,'' Maggert said. ''I really felt like I hadn't lived up to the way I should have been playing.''
He broke the tournament 36-hole record of 15 under set by Rocco Mediate in his 2013 victory.
Paraguay's Carlos Franco was second, also shooting 63.
''Jeff Maggert is a good friend of mine, too, and he played well,'' Franco said. ''I know he's a fantastic player, but I'm prepared to come strong tomorrow.''
Bernhard Langer was third at 10 under after his second 65. The 59-year-old German star won the Boeing Classic last week in Washington for his fourth victory of the year and 29th overall on tour. He has played 49 holes without a bogey dating to the final round in Washington.
''There's this guy from Germany that's lurking around the lead again, too,'' Maggert said. ''I have to play well tomorrow.''
''Maggert's a tough competitor. When he plays well, he doesn't make a whole lot of mistakes,'' Allen said. ''It's going to be hard to catch him, that's for sure.''
Tom Watson followed his opening 65 with a 72 to drop into a tie for 38th at 3 under. On Friday, Watson broke his age for the fourth time on the tour. He will be 67 on Sunday.
''Golf swing wasn't really very good today,'' Watson said. ''I hit a lot of bad shots today. I got what I deserved. I tried as hard as I could, but the swing just didn't work very well.''
Mark O'Meara withdrew after nine holes because of back problems.