His 16-under 126 total is only three shots shy of the PGA Tour record low score for the first 36 holes, set by Justin Thomas at the Sony Open in Hawaii in January.
Fellow Australian Day had a "lucky" hole-in-one en route to a 65, while American Fowler carded 64 to share second place at 13-under.
Leishman is six strokes clear of fourth-placed Patrick Cantlay in the penultimate event of the PGA Tour season.
Leishman said his goal had been to "try to do the same as yesterday, give myself heaps of opportunities and then try to take advantage of them."
He did that and then some, his confidence boosted by his birdie at the par-four seventh, where he struck a low fizzing pitch that scuttled into the hole.
"It had a bit of speed and then in she goes. You go from scrambling for a par to making three (birdies) in a row," said the laid-back Leishman.
The world number 22 has won twice on the PGA Tour, including the Arnold Palmer Invitational in Florida in March.
Leishman cannot, however, boast the best halfway score ever at Conway Farms, an honour that belongs to Day, who plundered the layout two years ago on his way to a victory that vaulted him to number one in the world.
Day's seven-iron at the 188-yard 17th on Friday landed in the rough just in front of the green, took a couple of bounces and trickled into the hole, much to his surprise.
"We were trying to land it 182 (yards) and I kind of pushed it. It was a lucky hole-in-one, I guess," Day said after his second ace on tour.
He also had an eagle, a chip-in from 30 feet from beyond the green at the par-five 14th.
"(I am) very pleased with how the last two days went," Day said. "I can't get too far ahead of myself. Last time I was here I was five shots better (after 36 holes). I've got to somehow try to catch up to my number. That's the main goal."
Fowler also finished with a rush, picking up five strokes in the final six holes.
The BMW Championship is the third of four playoff events on the PGA Tour. The top points earner after next week's Tour Championship will receive a $10 million bonus awarded to the season-long FedExCup champion.
Points leader Thomas carded 70 to fall 11 strokes behind Leishman. Second-placed Spieth also shot 70 to trail by nine.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Christian Radnedge/Gene Cherry)
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