The British duo set the timing screens ablaze throughout the 41.5-kilometre test from Arc-et-Senans to Besancon in an incredible show of strength.
Wiggins, resplendent in the yellow skinsuit was quickest through both intermediate splits before setting a final time of 51 minutes and 24 seconds, 35 up on Froome to ensure a Team Sky 1-3 at the top of the general classification.
Cadel Evans (BMC Racing) fought hard and placed sixth on the day, 1:43 down on Wiggins to split the pair heading into the race day. Wiggins now holds an advantage of 1:53 over the Australian with Froome just 14 seconds further back.
Earlier Fabian Cancellara (RadioShack-Nissan) had laid down a marker on the rolling course with a time of 52:21 but the Swiss rider was unable to fend off Wiggins and Froome, his time holding on for third quickest on the day.
After claiming his first Tour de France stage victory Wiggins admitted the GC was the main objective of the day.
He said: "We're nine days into the Tour now and there were two tough stages before today. Everyone was tired last night and you never know how you're going to recover.
"Time trialling's what I do best though. I get into my zone, know exactly the routine I have to go through during the stage and I felt great today. The minute I turned the first pedal stroke on the warm-up I felt fantastic so I knew I was on a good one.
"This is what we've trained for. Sean was saying to me on the radio in the last 10km - 'think of all those hours, all those sacrifices you've made' - this is what that was all for and that really motivated me.
"All the hard work during the winter, missing my children's birthdays being on training camps and things - this is what it's all for - these moments.
"I didn't set out today for the stage win, it was a battle fore the GC, but to get the stage win is a bonus and that's fantastic as well."
Backing up a sensational time trial performance at last year's Vuelta a Espana, Froome was also happy to clock such a competitive time.
"There's no tactics on days like today," he said. "Time trials are by far the hardest event in cycling. You just have to go as fast as you can and turn yourself inside out to get the best time possible.
"In terms of the race information I was getting in my ear, it's good to know you're putting in a fast time but then you've also got to be careful you've not started too fast and overcook it so it's a very fine line to gauge that effort.
"Bradley's time was quite a bit faster than mine but I'm really happy with the performance I put in. I gave it everything I had and that's all I could do. It was a big performance we put in and there could be a bit of a celebration later.
"There's still a long way to go before I can start thinking about a podium position, I'll just take it day by day from here."
Fastest of the early runners, Tony Martin (Omega Pharma-Quickstep) saw his run of bad luck continue as the world time trial champion punctured shortly after the start. The German was still able to set the quickest time, but his effort was immediately under threat.
Cancellara swept to the top of the standings for the time being but was run extremely close by Tejay Van Garderen (BMC Racing), the young American going quicker through the splits before giving way at the line. Fourth on the stage was enough to move the 23-year-old back into the white jersey.
Leading final positions after Stage 9 (Arc-et-Senans - Besancon (ITT), 41.5km): 1 Bradley Wiggins (Gbr) Sky Procycling 51mins 24secs, 2 Christopher Froome (Gbr) Sky Procycling at 35secs, 3 Fabian Cancellara (Swi) RadioShack-Nissan at 57, 4 Tejay van Garderen (USA) BMC Racing Team at 1.06, 5 Sylvain Chavanel (Fra) Omega Pharma-QuickStep at 1.24, 6 Cadel Evans (Aus) BMC Racing Team at 1.43, 7 Peter Velits (Svk) Omega Pharma-QuickStep at 1.59, 8 Vincenzo Nibali (Ita) Liquigas-Cannondale at 2.07, 9 Denis Menchov (Rus) Katusha Team at 2.08, 10 Andreas Kloden (Ger) RadioShack-Nissan at 2.09, 11 Maxime Monfort (Bel) RadioShack-Nissan at 2.15, 12 Tony Martin (Ger) Omega Pharma-QuickStep at 2.16, 13 Haimar Zubeldia Agirre (Spa) RadioShack-Nissan at 2.20, 14 Rui Alberto Faria Da Costa (Por) Movistar Team at 2.22, 15 Janez Brajkovic (Slo) Astana Pro Team at 2.26, 16 Jens Voigt (Ger) RadioShack-Nissan at 2.44, 17 Lieuwe Westra (Ned) Vacansoleil-DCM Pro Cycling Team at 2.45, 18 Tony Gallopin (Fra) RadioShack-Nissan at 2.46, 19 Jeremy Roy (Fra) FDJ-Big Mat at 2.52, 20 Jerome Coppel (Fra) Saur - Sojasun at 2.54
Selected others: 36 David Millar (Gbr) Garmin - Sharp at 4mins 14secs, 39 Stephen Cummings (Gbr) BMC Racing Team at 4.23, 161 Mark Cavendish (Gbr) Sky Procycling at 8.43
General classification after Stage 9: 1 Bradley Wiggins (Gbr) Sky Procycling 39hrs 09mins 20secs, 2 Cadel Evans (Aus) BMC Racing Team at 1min 53secs, 3 Christopher Froome (Gbr) Sky Procycling at 2.07, 4 Vincenzo Nibali (Ita) Liquigas-Cannondale at 2.23, 5 Denis Menchov (Rus) Katusha Team at 3.02, 6 Haimar Zubeldia Agirre (Spa) RadioShack-Nissan at 3.19, 7 Maxime Monfort (Bel) RadioShack-Nissan at 4.23, 8 Tejay van Garderen (USA) BMC Racing Team at 5.14, 9 Jurgen Van Den Broeck (Bel) Lotto Belisol Team at 5.20, 10 Nicolas Roche (Irl) AG2R La Mondiale at 5.29, 11 Rui Alberto Faria Da Costa (Por) Movistar Team at 5.46, 12 Rein Taaramae (Est) Cofidis, Le Credit En Ligne at 5.56, 13 Tony Gallopin (Fra) RadioShack-Nissan at 5.59, 14 Janez Brajkovic (Slo) Astana Pro Team at 6.29, 15 Andreas Kloden (Ger) RadioShack-Nissan at 6.33, 16 Sylvain Chavanel (Fra) Omega Pharma-QuickStep at 8.18, 17 Frank Schleck (Lux) RadioShack-Nissan at 8.19, 18 Jerome Coppel (Fra) Saur - Sojasun at 8.31, 19 Levi Leipheimer (USA) Omega Pharma-QuickStep at 8.34, 20 Peter Velits (Svk) Omega Pharma-QuickStep at 8.44
Selected others: 109 Stephen Cummings (Gbr) BMC Racing Team at 41mins 58secs, 132 David Millar (Gbr) Garmin - Sharp at 51.47, 153 Mark Cavendish (Gbr) Sky Procycling at 1:00.42