Greipel capitalised on a strong lead out to dominate the field sprint at the end of the 176.5km stage from Aix-en-Provence to Montpellier.
The powerfully built Lotto-Belisol rider won ahead of points classification leader Peter Sagan (Cannondale) and stage one winner Marcel Kittel (Argos-Shimano).
“The whole day was a really nervous one," said Greipel. "With the wind everybody seemed afraid that it might split.
"But for me the sprint was a close one but the team was there for me and they supported me well for the lead-out and I think they were going pretty fast."
Impey kept the yellow jersey in the Orica-GreenEDGE family and he now leads the race ahead of Edvald Boasson Hagen (Sky), with team-mate and former race leader Simon Gerrans third.
“It'll sink in tomorrow but I think it's going to be amazing to ride in the Tour de France as the leader," said Impey. "I'm going to be on a high the whole way to the finish and hopefully I'll feel like I'm floating."
The South African capitalised on a late split in the peloton which saw Gerrans finish several seconds behind the stage winner.
“Simon is probably one of the most selfless riders out there. He's a great champion and he's always willing to commit to everyone around him, today was proof of that," said Impey.
"We were riding for (Matt Goss) Gossie today and obviously it didn't work out but with me being the final lead-out man it worked out the way it has. I wouldn't say that I stole the jersey, I like to think that we are sharing it.”
The flat, fast and windy stage was kept under a tight leash with only a 43km solo breakaway by Luis Angel Mate of Cofidis providing early interest before his efforts ended.
An early taste of the sprint battle to come arrived at the only intermediate sprint of the day, where Andre Greipel took the major points ahead of stage five winner Mark Cavendish (Omega Pharma-QuickStep), Alexander Kristoff (Katusha) and Sagan.
From that point the peloton appeared to be more interested in battling the strong crosswinds than each other, with the race effectively neutralised until the finale.
With 35km to go Cavendish was involved in a crash but quickly remounted and rejoined the peloton eight kilometres later to contest the finish.
“I don't know if Mark Cavendish was hindered by his fall, he was there at the finish," said Greipel. "I think he is okay because he is sprinting. He won yesterday and I won today and I think it's good because it's our objective to win stages.”
The run in to Montpellier was initially controlled by Cavendish's Omega Pharma-QuickStep team, then Argos Shimano, but it was the experienced and disciplined Lotto-Belisol squad who delivered the race to its leader, Greipel.
“It's nice to hear that (Peter) Sagan thinks it was impossible for him to win against me," said Greipel.
"Yesterday I hesitated a little bit in the sprint but today I really went for it and the team did too and of course I'm really proud to win again, the day couldn't have ended better."
The seventh stage is a 205.5 km ride from Montpellier to Albi. The race's first mountain stages will be held in the Pyrenees on Saturday and Sunday.
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