Garcia held a one-stroke lead from American Roberto Castro and Sweden's Henrik Stenson at a low-scoring TPC Boston on Saturday.
Garcia, only opted to play in the tournament because he risked missing the next cut in the FedExCup playoffs and he eagled the 18th hole to complete an impressive seven-under-par round of 64, leaving him at 13-under for the tournament.
The Spaniard's only major hiccup came on the par-four 14th where he double bogeyed as did Castro.
Stenson was immaculate as he recorded a bogey free eight-under par 63, a round matched only by England's Justin Rose, the U.S. Open champion who also avoided bogeys as he moved within four shots of the lead.
Overnight joint leader Phil Mickelson was unable to progress from his first round 63. He shot an even-par 71 after some wayward driving - albeit with characteristic recovery work - on the back nine where he made two bogeys and a double as well as a pair of birdies.
CLASSIC SHOT
Mickelson did produce the shot of the day however. His chip from a poor lay in rough over the back of the 11th green landed two feet from the pin for a tap-in par after the left-hander produced a remarkable amount of back spin.
It was classic Mickelson, as he acknowledged after his round.
"I've not seen anybody else hit that shot, to be able to spin it back from that distance and lob it. It sure looks good," he said.
"I could describe it, but nobody is going to understand that. It was a really good shot," added the British Open champion.
World number one Tiger Woods, playing with Mickelson and Masters champion Adam Scott, shot a four-under 67, with just one bogey as he ended up a stroke behind Mickelson at the end of their 36 holes together.
But Woods was disappointed with his work on the greens.
"I had a hard time hitting the putts hard enough. They were a little slower this afternoon, obviously with the mist coming in, it definitely slowed it up," he said, after finishing his round in drizzle.
"But still, I just didn't hit them hard enough. And they were snagging at the grain a little bit at the end. And a couple of putts I thought I poured, but they got snagged at the end."
Garcia made a blistering start to his round, with some superb ball-striking, recording five birdies and no bogeys as he reached the turn in 31.
GOOD DECISION
Soft greens again made for low scoring and Garcia was clearly happy to have pushed himself to play in the tournament in order to make sure he was in the third event in the playoffs.
"It was touch and go if I was going to make the BMW Championship without playing here. Obviously being 55th ‑ 16 guys could easily pass me if they played well.
"We decided to come here and make a little bit of an extra effort of playing obviously five weeks in a row, which I don't usually enjoy very much.
"Hopefully I'll be able to play well the next couple of days and give myself a good shot at it," he said.
PGA Championship winner Jason Dufner put himself in the frame with a second round of 66 taking him to within three shots of the lead alongside fellow American Matt Kuchar.
Exciting rookie Jordan Spieth and another young American Harris English were both four shots off the lead.
Defending champion Rory McIlroy shot even-par for the day to leave himself well back, 12 strokes away from Garcia.
(Reporting By Simon Evans,; Editing by Gene Cherry)
