The Italian national champion now leads the Tour by six seconds from Froome, with Frenchman Bardet closing to within 25 seconds of yellow in third.
Upbeat: Michael Matthews hasn't won a stage at this Tour so far, but is confident the final week can bring him a victory. Marcel Kittel has made the best of the whittled competition and won 5 stages, out sprinting pre-race green jersey favourite Andre Greipel. He is expected to attack in Thursday's 12th stage, a 214.5-km trek featuring three major climbs and a summit finish in Peyragudes.
End result: Sky has two riders - Froome and Landa - in the top five.
"This shows that Froome is beatable", exhorted Alexander Vinokourov, Aru's Astana team manager.More news: Female Afghan Robotics Team Gets Donald Trump Assist
"The pace was very high all day long, but just in the last meters, I saw Froome was in trouble and I just try to go to the line as soon as possible", Bardet said.
Landa is now fifth, 1:09 behind Aru, and Team Sky's management will need to make clear who the leader is after the Spaniard, whose contract expires at the end of the year, finished ahead of Froome on Thursday.
By stark contrast it was a miserable day for Astana's Jakob Fuglsang, who withdrew from the race with a fractures to his wrist and elbow he suffered on Stage 11.
George Bennett is the leading Kiwi rider on this year's Tour de France.
And having seen its tactics work this time, Sky is already planning its next move to put Froome back in the yellow jersey he held for seven days before Aru took it - with Landa as the team's new joker.
"It's flawless for us", Froome said.
But on the ultra-steep final ascent to Peyragudes airfield, when Aru launched an explosive attack and then France's Romain Bardet followed him up the road, Froome veered right as he struggled to keep his gear turning.