Wi has won eight times in Asia and once in Europe, but the best he has done on the American circuit has been four runner-up finishes.
He shot a 3-under 69 at the Pebble Beach Golf Links to reach 12-under for the tournament. Two-time former champion Dustin Johnson was alone in second place at 9-under after shooting a 72 at Spyglass Hills.
Tiger Woods, making his U.S. debut this week, recorded his second straight 68 and was at 6-under in a tie for 17th place. Woods played Friday at the Monterey Peninsula Country Club, which unlike the other two courses being used for this event has a par of 70.
Phil Mickelson shot a 65 at Monterey Peninsula and was among those tied for eighth at 7-under.
Harrington and J.P. McManus owned a seven-shot lead in the pro-am portion of the tournament.
New England Coach Bill Belichick, playing in the tournament after coming up on the short end of last Sunday's Super Bowl, teamed with Ricky Barnes to shoot a 60 Friday and they moved into a tie for seventh place.
A win by Wi would give the PGA Tour two debut winners in a row. Kyle Stanley won his first event last week in Arizona after letting a six-shot lead get away the week before at Torrey Pines. Stanley, who leads the early standings in the FedEx Cup points race, is not playing this week.