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Wilson, an American who has already won titles in Phoenix and Hawaii this year, shot a 66 to match the Englishman atop the leaderboard at 11-under par 131 after 36 holes at the penultimate event of the US PGA playoff series.
Only the top 30 players in the season-long points chase after Sunday's final round will advance to the season-ending Tour Championship in Atlanta and have a chance to capture the $10 million playoff prize.
Rose, who opened with a 63, was intent on adding the $1.44 million top prize from this week's $8 million tournament before worrying about next week.
Rose, who won the Memorial and National last year for his first US PGA triumphs, birdied the par-4 third and answered a bogey at the par-4 seventh with back-to-back birdies to finish the front side.
He took another bogey at the par-4 13th but responded with an eagle at the par-5 15th and a birdie at the par-4 16th to claim the lead, only to stumble back with a bogey at the last.
Even so, he was pleased with the day.
"You never quite know what to expect after playing so well in the first round," Rose said. "Actually, my caddie said it's the best round he's seen in 20 years out there from a ball-striking perspective.
"So, there's only one way to go from there. But today(Friday) was good."
Wilson opened with his lone bogey of the day, then birdied the par-4 fifth and ran off a streak of four birdies in a row ending at the par-5 11th before adding a final birdie at the par-5 15th.
Wilson is assured a spot at the Tour Championship.
But a victory here would give him a spot on the Presidents Cup team and perhaps a crack at player of the year.
"That would put me with the most wins of anybody, and then going into East Lake if I can get another one there, I think I'd have a good argument," he said.
"That's a lot of 'ifs,'" he acknowledged. "I've played great so far. There are a lot of great players out here, but I feel like I'm playing very close to the same form I had when I started the year out. My mind is in a better place, and I'm just kind of accepting the results."
American Webb Simpson, the overall points leader after a victory last week, stood third on 133, one stroke ahead of Australian John Senden, who fired a 66.
Australian Robert Allenby and American Bill Haas shared fifth on 136, one stroke ahead of Aussie Geoff Ogilvy and Americans Brandt Snedeker, David Toms, Matt Kuchar and last month's PGA Championship winner, Keegan Bradley.
Tee times have been moved up for the third round, with the leaders to tee off at 16:15.
"It’s going to be fresh, cold," Rose said. "I don’t mind that, though, to be honest with you. Historically, I’ve played pretty well in the mornings."
Leading scores on Friday after the second round of the $8 million US PGA Tour BMW Championship (USA unless noted, par-71):
131 - Mark Wilson 65-66, Justin Rose (GBR) 63-68
133 - Webb Simpson 65-68
134 - John Senden (AUS) 68-66
136 - Bill Haas 70-66, Robert Allenby (AUS) 69-67
137 - Geoff Ogilvy (AUS) 69-68, Brandt Snedeker 71-66, Keegan Bradley 71-66, David Toms 71-66, Matt Kuchar 72-65
138 - Gary Woodland 70-68, Jim Furyk 68-70, KJ Choi (KOR) 67-71
...
139 - Brendon de Jonge (ZIM) 75-64
140 - Robert Karlsson (SWE) 69-71
141 - Camilo Vilegas (COL) 73-68, Rory Sabbatini (RSA) 72-69, Charl Schwartzel (RSA) 73-68, Martin Laird (GBR) 72-69, Luke Donald (GBR) 75-66, Sergio Garcia (ESP) 69-72
142 - Aaron Baddeley (AUS) 71-71, Jason Day (AUS) 77-65, Marc Leishman (AUS) 71-71, YE Yang (KOR) 70-72, Carl Pettersson (SWE) 70-72
143 - Andres Romero (ARG) 77-66, Ernie Els (RSA) 72-71
144 - Brian Davis (GBR) 74-70, Adam Scott (AUS) 74-70
145 - Fredrik Jacobson (SWE) 72-73
146 - Jhonattan Vegas (VEN) 73-73
151 - Vijay Singh (FIJ) 76-75
