First-round leader Johnson shot 3-under par 67 and Flanagan had a 7-under 63 Friday to share the second-round lead at 10-under at the U.S. Bank Championship over the 6,579-yard Brown Deer Park Golf Course.
Kent Jones and Gavin Coles were tied for third a shot back of the leaders. Jones shot 65 and Coles, of Australia, had the low round of the tournament at 62, one shy of the course record.
Another stroke back at 132 were Troy Matteson and Ken Duke, who both shot 65.
Despite retaining a share of the lead, Johnson was upset he had two major lipouts on his final two holes to deny him outright possession of first. The hardest to bear was a putt of just under 10 feet on the par-4 ninth hole.
It was a really nice putt, Johnson said. It would have been nice to get to 11.
Because Johnson missed the putt, Flanagan caught him with a 12-foot birdie putt on the ninth, which was also his final hole.
Flanagan was delighted to be tied for the lead after struggling in his rookie season. He was promoted to the PGA TOUR after winning three times last year on the Nationwide Tour.
Its really been a bit of a struggle, he said. I have not been intimidated out here. Its just learning the golf courses. And my swing just hasnt been cooperating with me.
In a group of seven players at 133 was defending champion Joe Ogilvie, who had a 67 to remain in contention to become the first player to win back-to-back titles.
Im not in it to lose it, Ogilvie said. I like breaking streaks, especially those type of streaks.
South African brothers Deane Pappas and Brenden Pappas, who trailed Johnson by a stroke after the first round, slipped down the leaderboard. Brenden shot even-par 70 for a 134 total while Deane had 72 for 136.
The cut was 2-under par 138 and 78 players made it.
Kenny Perry shot 68 for a 5-under total of 135 to easily make it to the weekend in a tournament he won in 2003. Perry, who captured last weeks John Deere Classic, has a chance to win for the fourth time this season.
Perry has been criticized for skipping the British Open also being held this week. He wants to make the Ryder Cup team because the event this September is being held in his native Kentucky. He felt he had a better chance to earn cup points here.
However, Perry was not worried that doing well in this tournament would validate his decision to other people.
I dont know. I mean, Im doing what Im going to do. Im not listening to nobody else. Period, he said.
It is always hard to follow up a low round like Johnsons opening 63 with another good one. But even though Johnson missed two key putts at the end, he managed to shoot 67 because of two long ones he made earlier'28 feet on the sixth hole and 34 feet on the 13th hole.
Flanagan matched Johnsons opening 63 despite a slow start. He began with five pars before he birdied seven of his remaining 13 holes.
I stayed patient and I really played well on the back nine, he said.