A closing par left the Swede on nine-under 131 and gave him the 36-hole outright lead for the first time in 185 starts on the PGA Tour.
"I think I played pretty good this year," Blixt told reporters. "Obviously not had the good finishes yet."
Four times this season he has entered the weekend in the top-10 but faltered.
"The test is going to be this weekend," he said, "if I can have a good weekend or not."
Na (62) and first-round leader Finau (68) shared second at eight-under 132.
Na, playing in the morning like Blixt, started off with an eagle at the first and added six birdies in his blistering round.
"Yeah, I like this golf course," said Na, after his third 62 or lower at Colonial.
"Fits my game. You've got to take advantage of those weeks because there is not too many golf courses like this on tour anymore."
Finau finally provided some competition in the afternoon, despite increasing winds, with three birdies and a bogey in his last nine holes.
Slovakia's Rory Sabbatini (66) held fourth at six-under with former champion Jordan Spieth (70) in a group of five at five under.
Spieth, often missing fairways, wound up with five bogeys before collecting birdies on two of his final three holes. He also had a 50-foot birdie putt at the 10th and a 46-footer two holes later.
"It was a grind," Spieth said. "I would like to think -- I hope, I hope -- and it felt like today was kind of the off day in a four rounds.
"I just -- you know, towards the end of yesterday's rounds kind of lost a little bit of the feel in my swing that I had Tuesday, Wednesday, beginning of Thursday, and I didn't really find it today."
Jason Dufner (68), who at one time had a chance to take the lead, was in the group at five-under. Three bogeys in his final four holes soured a sparkling round that included five birdies.
World number three Justin Rose, the defending champion, shot 67 to avoid the two-over cut by a stroke while Rickie Fowler (three over) and Bryson DeChambeau (four over) were not as fortunate.
(Reporting by Gene Cherry in Raleigh, North Carolina; Editing by Peter Rutherford)
