"It's hard to pinpoint exactly, but with about three laps to go on the climb my stomach was really, really upset with me.
"I had to make an emergency stop in the pits. For me it was super-upsetting because I was on such a high with the Tour de France. To perform with distinction there and then end here with such a low.
"I just had bad, bad, bad diarrhoea. Once I had one movement, I was done."
Henderson said that sometimes when you are afflicted during a stage race, you have enough time to work through it, so to speak, and recover. The pace was too hot for that to happen here.
Henderson, who will have a week off the bike before returning to work with his Lotto-Belisol team, took comfort in the performance of Bauer.
The 27-year-old had asked Henderson when he could start looking for moves and he told him to wait for the next attack and then go.
"It was perfect. What an amazing ride," Henderson said.
There will be many pundits questioning Great Britain's tactics that saw them hold everyone out of the breaks to work for Mark Cavendish, but Henderson will not be one of them.
He even revealed team captain David Millar had spent some time in the morning canvassing other teams to try to drum up support in the peloton.
"It was everything for Cavendish. There was no way they were going to compromise that. They were just praying for more help.
"They came around this morning asking me how Jack was feeling and saying that this was 'obviously a good course for you, Greg.'
"I spoke with [Andre] Greipel later and he said [Millar] had already spoken to Germany. He was trying to get as much help as possible because he knew it was going to be difficult to control.
"I said, 'I hope Jack's good, I hope he'll be in the break.' And he was."
