Porte was Sky co-leader already, says Thomas
Britain's Christopher Froome (L) and Australia's Richie Porte ride during a training session of the Britain's Sky cycling team on July 3, 2014 in Leeds - by Eric Feferberg
The Welsh rider said number two Richie Porte had started the day as co-leader before Froome even pulled out, after crashing twice on the stage.
Sky team manager Dave Brailsford insisted Froome's withdrawal was due to the injuries he suffered from his crashes on Wednesday's stage five from Ypres in Belgium to Arenberg Porte du Hainaut.
But Froome suggested in a Twitter post that it was the pain he suffered in a fall on Tuesday, in which he injured his wrist, necessitating his wearing a splint on Wednesday, that had been the reason he kept falling.
"Devastated to have to withdraw from this years TDF. Injured wrist and tough conditions made controlling my bike near to impossible," he said.
Thomas, though, said Sky had already put into practice a contingency plan, despite insisting before the Tour that all their eggs were in one basket.
"To hear Froomey crashed early on, it was 'not again' sort of thing," said Thomas.
"I think he was just behind me when he crashed again and when I heard it I thought 'that sounds nasty' and then I heard on the radio it was Froome so it wasn't good.
"But we knew going into today we had Richie as well and it was a kind of two-pronged attack.
"They were both on an equal footing in the team so it changed then for Richie and so I think it was a pretty successful day really when you look at that."
Inevitably, questions turned to the non-selection of 2012 Tour winner Bradley Wiggins, but Brailsford insisted the team had done the right thing.
"We picked a team at the time with all the data we had. Chris was the best bet to try to win this race, he was in better shape than last year," said Brailsford.
Wiggins himself was in no mood to gloat.
Speaking via his agent, he said: "It's a tough day. I never like to see a great racer go down but Chris will be back.
"Today has showed how hard it is to win the Tour de France, but the team will have prepared for this and they'll deal with it."
Brailsford suggested as much with his attention turning immediately to Porte, who is eighth overall and 1min 54sec behind race leader Vincenzo Nibali of Italy after Wednesday's stage.
"We're very happy to have Richie up there in GC and the fight in the mountains lies ahead, and we want to get to those mountains as soon as possible," he said.
"It's not to be (Froome's) year but in Richie Porte we've got a very capable guy who will now lead the team.
"I think like anything else, on a day like today when you have a setback, you've got to roll with it.
"It's part of sport, you've got to recalibrate your goals and go again. You might take a punch but you get up and go again.
"In Richie Porte he's come into this team, we've selected him to be the number two, he had great ability today and great courage with Geraint to ride the cobbles the way he did and given the way it's timed at the minute, we've got an exciting couple of weeks to come."
Thomas did a sterling job for Porte in the final two cobbled sections of Wednesday's stage.
They had been in the same group as Alberto Contador, who lost 2min 35sec to Nibali, but took 43 seconds out of the Spaniard after a great push from Thomas.
"I saw Contador was struggling a bit on the cobbles on sector four and three, so I said 'Richie get on my wheel, we'll smash it and see what happens'," said Thomas.
"It was good fun but obviously losing Froomey is not good, but Richie I think, he's in good form."