He edged out main rival Contador by nine seconds in Wednesday's individual time trial to Chorges.
The weather held off just enough for Froome to beat the Spaniard Contador, who had taken a much more aggressive approach to the mountainous time trial route on slick roads with rain falling intermittently.
With Bauke Mollema well off the pace, Contador moves into second place but his deficit to Froome now stands at four minutes 34 seconds heading into Thursday's much-anticipated double ascent of the Alpe d'Huez.
The weather had threatened to play a major role as it began to rain on the mountain tops midway through the day, with a few claps of thunder heard.
The worst of it had been forecast for around half an hour before Froome was due to start - the last of today's riders - but while Froome was clearly being careful on the greasy surfaces, he was not majorly troubled.
Contador was in attack mode, frequently out of the saddle and ahead of Froome through all three intermediate checkpoints.
But where Contador stuck with his road bike throughout, Froome had changed to his time trial bike midway through the stage and was 20 seconds quicker than his rival over the final 13 kilometres.
As well as increasing his overall lead, the victory makes Froome only the second Briton to have won more than two stages in any one Tour, with Mark Cavendish the other.
There were clear reminders of the dangers posed by the course and the conditions on it.
Jean-Christopher Peraud of AG2R La Mondiale began the stage despite suffering a small fracture to his clavicle when he came off during a practice ride of the route this morning, and he then crashed again two kilometres from the finish, forced to abandon the Tour from ninth place overall.
The same corner saw Mollema crash into the barriers but remain upright, while Roman Kreuziger had a major wobble before his team-mate Contador took it much more carefully.
With the weather easing before the main contenders attacked the course, the lead changed several times late on.
Alejandro Valverde had sent the standard which Contador beat by less than a second before in turn being trumped by Froome.
Mollema could only manage 11th place, two minutes nine seconds behind Froome's time of 51m 33sec, and drops to fourth overall behind Contador and Kreuziger.
On Tuesday night Froome had accused Contador of riding dangerously when the Spaniard crashed on the descent of the Col de Manse approaching Gap, almost taking Froome out with him.
But Contador defended his actions by insisting he would continue to push hard all the way to Paris with the two-time winner having no interest in a runners-up spot.
With Froome taking a no-risk approach on the slippery surfaces, Contador looked much the more aggressive man throughout today's stage, and had led by 20 seconds at the second time check, 13.5km into the stage.
But that advantage had dropped to 11 seconds by the third at 20km, despite Froome stopping short of the line to change to his time trial bike - a tactic adopted by several riders today, but not by Contador.
Tony Martin, the world time trial champion who beat Froome by 12 seconds in the first race against the clock last week, was more than three minutes off the pace - the mountainous terrain on Wednesday not to the German's liking.
Cavendish's time of a little over 59 minutes was 7mins 35sec off the pace by the finish, but the Manxman was satisfied with that after suffering an upset stomach on Tuesday , his sights now firmly set on the final stage into Paris.