The incident less than 20km into the stage cost Wiggins far more time than the 10 seconds by which he finished second to compatriot Alex Dowsett, and robbed Wiggins of the momentum that he had built up.
Wiggins had set a storming pace, but was over a minute behind at the first intermediate split at 26km of the 55km stage.
It also emerged that the Tour de France winner and Olympic time trial champion had been suffering from illness, yet despite that he managed to haul himself back in the second half of the stage almost enough to claim victory - though predictions that he would beat race leader Vincenzo Nibali by a minute or more.
It was just the latest blow at the race for Wiggins, who was involved in a crash in wet conditions on Friday's seventh stage, and had been held up by another crash on Tuesday's fourth stage.
That series of frustrations clearly caught up with Wiggins on Saturday, and he fairly threw his bike into the undergrowth at the side of the road as he waited for one of the support team to come up with a new machine.
"I think there was some initial disappointment because I wanted to win the stage," Wiggins admitted.
"It’s been a challenging few days with the crash yesterday and then to come back up. It wasn’t an easy course. I’ve said all along that it wasn’t one of those ones where you could take three or four minutes out of people because it was so technical at the start.
"Then obviously to have a puncture and have to change bikes and disrupt the rhythm is never going to help.
"But then the second part of the course was really suited to me and I took back a lot of time on people there. It is what it is and it’s put us right back up there now. It’s going to be a hell of a race for the next two weeks."
Over the 55km distance the 33-year-old added that it was important to gauge the effort and to look to have something in reserve for the final kilometres.
“I think I rode it pretty well," he continued. "I was a bit ruffled after the bike change and didn’t get the best out of myself on that technical part of the course. It was a bit damp still as well so I was a bit cautious – especially after crashing yesterday.
"But from Pesaro onwards I really got into my stride and I think physically I was as good as I’ve ever been. But it is the way it is. We’ll deal with it now, but I’m pleased at the same for Alex Dowsett. It’s a brilliant start to his Grand Tour career."
The dynamic of the race is now set to change as Astana defend the jersey, but Wiggins is refusing to rule out a challenge for overall victory.
“There are two weeks to go. The last week’s going to be very difficult and the time gaps are relatively small still," he added.
"A minute and 16 to Nibali still with all the problems yesterday isn't that bad it’s all to play for. It’s not easy to defend a Grand Tour lead so it’s not a bad position to be in.
"We’re still here and we’ve got three guys in the top 10 now. We’ve got a few cards to play.”