Five days after team mate Jack Bauer was caught by the peloton a few metres from the line after a 222-km breakaway, the Lithuanian attacked on a short climb close to the finish and never looked back.
German John Degenkolb took second place seven seconds behind and Norway's Alexander Kristoff finished third after the main bunch was split by a late crash on roads made slippery by torrential rain earlier in the day. All the riders from the main pack were credited with the same time as the incident happened with less than three kilometres left.
"I was the first to crash, I did not know what happened," said Slovakian Peter Sagan, who had been tipped as one of the stage favourites. Nibali still leads France's Thibaut Pinot by 7:10 and another Frenchman, Jean-Christophe Peraud, who crashed but said he was fine, by 7:23, ahead of Saturday's decisive time trial, a 54-km solo ride between Bergerac and Perigueux.
Garmin-Sharp, without team leader Andrew Talansky after the American pulled out due to lower back pain, only had a stage win in mind.
They had Tom-Jelte Slagter in the day's breakaway and the Dutchman served as Navardauskas's launchpad after the climb.
"The plan was to attack in the climb and to have one of our riders in the breakaway so he could take a strong relay to help me," Navardauskas told a news conference.
"It's almost amazing to keep the peloton at bay," said Navardauskas, who had his team mate's misfortune in mind.
"Until the last 10 metres I was afraid to turn back," he added.
Navardauskas powered away from the pack on the fourth-category climb of the Cote de Monbazillac 13 kilometres from the finish.
Pinot's FDJ.fr team led the peloton in the descent and on the flat portion leading to the line, Cannondale and Tinkoff-Saxo chased the Garmin-Sharp rider who was 25 seconds ahead with five kilometres left.
With just under three kilometres remaining, Peter Sagan was involved in the crash as well as France's Romain Bardet who is fifth in the overall standings and his AG2R-La Mondiale team mate Peraud.
"I was caught in the crash, I tried to avoid it but I couldn't. Romain crashed in front of me," Peraud told reporters.
"Obviously the rain did not help, especially in a finale with a lot of turns and nervous sprint in the end. We crashed, it's classic."
Pinot, instead, was well placed by the front of the peloton and avoided the crash.
"We knew it would be a nervous stage, it was important to be near the front. I did not crash, it's all good," the 24-year-old Frenchman said.
(Editing by Ed Osmond)
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