On a day when strong winds plagued the later starters, Evans finished 44 seconds behind stage winner David Zabriskie (Garmin-Cervélo). Evans now leads Tony Martin (HTC-Highroad) by 18 seconds with only a 164 km road stage remaining.
"I'm very satisfied," Evans said. "Two weeks ago, I didn't do the classics races because of that training ride crash, so coming back here I didn't know where I was. But I worked hard with some good people around me and came back at a good level."
The Australian also praised compatriot Richie Porte (Saxo Bank Sungard) for his performance, finishing in second place, 2 seconds back on Zabriskie.
"[It's] nice to see the Tassie boy back near his best again," he said.
Evans last won this race in 2006. Saturday marked the second time he has pulled on a leader's jersey this season, following his overall victory at Tirreno-Adriatico last month.
"This is a race that has always suited me," the 2009 world road champion said. "I used to live here in Romandie, so I feel a bit at home. For BMC being a Swiss company, it's an important race."
Directeur Sportif John Lelangue said the BMC Racing Team will be vigilant on Sunday.
"I'm confident we have a full seven-man team who will be riding strong to defend the jersey," Lelangue said. "We have to be careful because it's a short, difficult stage. We're more worried about Alexandre Vinokourov [third overall, at 19 seconds] than Martin. He already proved he can make that kind of stage [like his win on Friday]."
Evans said he is hoping for "a safe group sprint into Geneva."
Meantime, Taylor Phinney and his stars-and-stripes BMC timemachine TT01 didn't fare as well. The U.S. national time trial champion crashed into a wall about 700 meters into his race against the clock.
"I think I got just a little too a too excited," Phinney said. "I did some damage to my cleat and shoes and hip and back, but my knees, elbows and shoulder are fine. For a crash, it probably looks terrible, but I didn't get too hurt."