Fowler also finished with a rush, picking up five strokes in the final six holes for a 64 and joining Day at 13-under 129, while first round leader Marc Leishman was still on the course.
Jason Day has produced a stunning hole-in-one to surge to second spot midway through the second round of the BMW Championship, but even that was not enough to haul in compatriot Marc Leishman. Very easy to throw a mediocre round in there.
Leishman, who opened with a 62, was at 16-under 126.
The 29-year-old came back from three bogeys to put in another spectacular performance with an eagle on the 14th, ending round two with a six-under 65.
"To have a lead is really nice but I showed (two weeks ago) a lot can happen on the back nine".
Meanwhile, Leishman carded eight birdies in a seven-under 64 round on Friday to extend his lead heading into the weekend.
Rory McIlroy knows that after his second round at the BMW Championship his slim chances of advancing to East Lake to defend his FedExCup title are as good as over.
The 33-year-old Leishman is 18 holes from his third PGA Tour victory and his second this year, following his win at the Arnold Palmer in March.
Masters champion Sergio Garcia enhanced his Tour Championship hopes with a third 68 in a row, and his current position of tied for 15th is projected to lift him to 27th in the standings, but Phil Mickelson needs to go low on Sunday despite joining Garcia on nine under with a 69. Others included in that mix are Scott Brown, Ryan Moore, Charley Hoffman, Chez Reavie and Matt Kuchar - who each shot a 67 on Saturday - and Patrick Cantlay (70).
Leishman birdied three of his opening four holes and cancelled out a bogey-five at the sixth with a hat-trick of gains from the seventh to reach the turn in 30.
"Generally, I say to my wife if I have a bad round, 'Just give me 10 minutes and I'll be all right", Leishman said. Tomorrow I got to try not to do that.
He had previously made three straight birdies at holes 8-10 and got back on the birdie train with a tap in birdie at the par-four 12th.
His day looked like being much better after a sensational eagle at the opening hole, Fowler nearly driving the green before putting in from the fringes.