The 194.5-kilometre ride from Macon-sur-Valserine marked a return to racing after Tuesday's tumultuous rest day in which a Cofidis rider was suspended by his team following his arrest by police in a doping probe.
For the first time in the Tour, the peloton scaled the 17.4-kilometre Grand Colombier pass - classified as one of the hardest climbs in pro cycling in part for two tough patches with steep, 12 per cent gradients.
Voeckler, the Europcar rider who wore the yellow jersey for 10 days last year, earned his third Tour stage victory in a decade-long career competing in cycling's premier race.
With a few kilometres to go, Voeckler dusted off the breakaway group, beating runner-up Michele Scarponi of Italy by 3 seconds. Jens Voigt of Germany - at 40, the oldest rider this year - was third, another 4 seconds slower.
"I really pulled this out with my guts," Voeckler said. "I only knew I'd won with about 5 metres left."
Voeckler said he didn't ride for about 10 of the 20 days immediately preceding the Tour start because of knee pain that still hasn't fully dissipated.
At several points during the stage, Wiggins came under attack from some of his biggest rivals — but nearly all failed to make up any ground. Italy's Vincenzo Nibali tried to surge ahead in a big descent; Belgium's Jurgen Van Den Broeck attempted to jump ahead on the day's big climb; reigning champion Cadel Evans tried to shake Wiggins near the end — but to no avail.
"It was pretty straightforward today," said Wiggins, the Team Sky leader. "Fortunately the break went pretty early and we didn't have to go crazy (chasing it) ... it all sort of went to script today, really."
An early breakaway group of 25 riders — all far back in the overall standings — set the early pace, chiseling out a lead of nearly eight minutes on Wiggins and the other contenders.
But as the riders started the big ascent, that breakaway bunch splintered. By the top, four were out in front: Luis Leon Sanchez of Spain, Italy's Michele Scarponi, Dries Devenyns of Belgium and Voeckler — who led them over the top. The pack was more than five minutes behind.
On the downhill, Nibali benefited from help from Liquigas teammate Peter Sagan and sped ahead, gaining a minute on Wiggins. But a mid-grade climb remained, and the Sky team erased Nibali's lead by the finish.
"We sort of gambled a bit that we'd be able to take them back in the valley, which we did," Wiggins said. "We knew he was going to do that, it's his ace card, and we were waiting for it, and it came.
"We just didn't panic."
Evans said he was perhaps a bit too hesitant as Nibali surged.
"Maybe it was a missed opportunity for something," the BMC leader said. "(But) Sky have built a team for exactly this course and these kinds of situations, so it leaves opportunities few and far between."
Doping cases past and present have cast a shadow over this Tour. Just days before the Tour, news emerged of an investigation by French state prosecutors into allegations of improper use of a controlled corticoid by Europcar in last year's Tour - claims the team has vigorously denied.
Voeckler said the stage win "is really special because we had criticism before the Tour, because it really hurt me."
Some fans in Belgium at the start of the Tour on June 30 booed Europcar riders in the wake of the news.
"In a small way, my victory today was an answer to that," Voeckler said.
The stage came a day after the arrest of Cofidis rider Remy Di Gregorio of France at his team's hotel as part of a doping probe in southern Marseille. The team has provisionally suspended him.
Wiggins finished the stage 3:16 behind Voeckler, in 13th place, in a group including most of his rivals in the quest to win the yellow jersey when the Tour ends in Paris on July 22.
With Wiggins under a close escort by his Sky teammates, only Van Den Broeck was able to erase 32 seconds with a surge late in the stage. The Belgian trails Wiggins by 4:48 in eighth place.
Overall, Wiggins leads Evans by 1:53. Wiggins' teammate, Christopher Froome, is 2:07 back in third place. Nibali is fourth, 2:23 back, and Russia's Denis Menchov is fifth, 3:02 behind.
Riders embark Thursday on what Wiggins called the hardest stage of the race this year - a relatively short 148-kilometre trek from Albertville to La Toussuire, but with two of the toughest climbs in pro cycling and an uphill finish.
Evans said he'll be looking for any opportunity.
"I think the attacking riders will be more rewarded tomorrow," said Evans, adding that he felt "a bit empty, a bit tired" after Wednesday's stage.
Eds: Associated Press writers Greg Keller and Samuel Petrequin in Bellegarde-sur-Valserine contributed to this report.