Stage 9 starts from the Spanish town of Vielha Val d'Aran and ending on top the uncategorized climb to Arcalis in Andora that covers 184.5 km (11.4.6) miles of journey.
Froome repelled a series of attacks, notably from Martin, on the monster climb to the ski resort of Arcalis and he said: "I was hoping to gain more time on my rivals, but I just made sure we closed any gaps and at least finished on the same time as them".
Elsewhere in the race, Adam Yates done well to hang onto the White Jersey he was awarded after the flame rouge collapsed on him stage 7; but for Alberto Contador it looks as though his bid for another Yellow Jersey looks to be over as he conceded another minute to Froome, and now stands 3mins12s down on his rival.
"This is a dream come true, I'm so exhausted that I can't even speak", said Dumoulin, who has now won a stage at all three Grand Tours in the past year.
"I did everything I could", said Contador, a Tour victor in 2007 and 2009 who is now 3:12 off the pace.
"We went through all states, " Bardet said. Martin sprinted in 14th, six minutes 37 seconds behind the solo victor Tom Dumoulin (Giant-Alpecin) and two seconds behind Yates, Froome and Quintana.
"It's awful to have crashed like this twice in the first week and to have lost so much time after working so hard to be here. Believe me, I did the best I can".
"It scared me", Team Sky director Dave Brailsford said.
The general classification contenders enjoyed a late battle on the final climb of the day, with several attacks taking place within the final five kilometres.
Martin reflected on a day that tested the resolve of the peloton with Alberto Contador, the two-time race victor, abandoning the race after suffering crashes and illness earlier in the week. "One minute we were pouring water over our heads and putting ice-packs down our backs, the next minute it was hailing", Froome said.
Froome gritted his teeth as he crossed the line, raising both arms in celebration then pumping his right fist emphatically.
The race for the polka dot jersey was perhaps the best side story of Stage 9.
"I still have to make another step, or two, or three to get to the level of these guys", he admitted.
A stage that began under a blistering sun and temperatures reaching 41 Celsius in Spain ended in Dantesque conditions with driving rain and even hail in Andorra.
Kreuziger is 12th overall, 34 seconds back.
Asked about the wet weather, Thomas added: "It's actually quite nice". George Bennett of New Zealand knocked down a fan blocking his way while coming around a tight turn.
Sunday's stage to Andorra was expected to hand the peloton yet another severe test, and the majority of the riders were likely already looking ahead to Monday's rest day. Then there is one more stage in the Pyrenees on Tuesday, a 197-kilometer (122-mile) leg from Escaldes-Engordany, Andorra, to Revel, France.