Sky suffered several hits today in the Tour de France's stage to Bagnères-de-Bigorres: Richie Porte slipped from second to 33rd overall and Vasil Kiryienka missed the time cut.
"It was a bit of a war today," Porte told journalists, including Cycling Weekly. "Everybody saw that; it was an amazing stage."
Movistar, Saxo-Tinkoff, Garmin and Belkin ramped up the pace and forced Sky out the back ahead and on the first climb.
Froome remained with the front riders, protected his yellow leader's jersey but lost a GC helper.
Porte started the Tour de France as Sky's plan B after winning Paris-Nice and finishing second while helping Froome win Critérium International and Critérium du Dauphiné.
That plan went out the window today.
The Tasmanian tried to chase, hovered around two to three minutes, and even once sat only one minute behind Froome's group.
"He sat up, though," Brailsford said. "We told him there's no point, sit up."
Brailsford believes Porte's effort yesterday to Ax 3 Domaines' ski station took its toll.
"It was unexpected, not often do we see Richie have a day like that. Whether it's the heat or who knows. Obviously, he went deep and paid for it today," Brailsford added.
"Yesterday we knew that we wanted Chris up the Pailhères, so Richie and Pete [Kennaugh] went deep to do that. To be fair, though, in a group of 30 or 40 riders, you'd expect us to have more than one rider."
Froome was able to fend for himself in the day, which covered five high-mountain passes and 168.5 kilometres, but fortunately finished on a downhill to Bagnères-de-Bigorres.
Kennaugh appears fine. He suffered scrapes from a crash on the Col de Porte-d'Aspet, but continued and finished. Vasil Kiryienka will be missed after he placed outside the stage's time limit.
Porte called it "just a bad day."
"There's still another two weeks to the Tour so I'm looking forward to moving on," Porte added.
"My climbing form is pretty good. I fought along there by myself and I'll be fine... It was a hard day for everyone, everybody and yeah... no stress."
Sky fortunately will be able to use Monday's rest day to recover. Froome looks ahead to the time trial on Wednesday to gain more time.
"People said yesterday that the race was done, which I wish it was, but we know that bike racing is unpredictable," Brailsford added. "We've got the yellow jersey, though, we've got a time trial coming up, we've got a couple of stages where we'll manage and then we'll be back into the mountains."
Listen to the stage nine podcast
Tour de France 2013: Stage reports
Stage nine: Martin wins stage as Froome fights to keep lead
Stage eight: Froome wins Tour mountains stage to take overall lead
Stage seven: Sagan scores first win of 2013 Tour
Stage six: Greipel wins as Impey moves into lead
Stage five: Cavendish wins; Gerrans keeps lead
Stage four: Orica win Tour's team time trial to put Gerrans in yellow
Stage three: Gerrans outpaces Sagan to take win
Stage two: Millar denied yellow as Bakelants takes spoils
Stage one: Kittel wins chaotic opening stage
Tour de France 2013: Podcasts
Tour de France 2013: Comment, analysis, blogs
Tour de France: 100 Tours, 1,000 stories
Tour de France 2013: Photo galleries
Stage nine by Graham Watson
Stage eight by Andy Jones
Stage eight by Graham Watson
Stage seven by Andy Jones
Stage seven by Graham Watson
Stage six by Andy Jones
Stage six by Graham Watson
Stage five by Andy Jones
Stage five by Graham Watson
Stage four by Andy Jones
Stage four by Graham Watson
Stage three by Graham Watson
Stage two by Graham Watson
Stage one by Graham Watson
Team presentation by Graham Watson
Driver cleared of killing cyclist after claiming 'no recollection' of fatal crash
The crash occurred in 2018, with the jury's verdict delivered yesterday
By Ryan Dabbs •
Here are six riders moving down from the WorldTour in 2022
Some pretty big names will be taking the step down as more teams look to build to a WorldTour licence in the coming years
By Tim Bonville-Ginn •