"From an emotional point of view, it was horrible. It's a horrible, horrible, horrible place to find myself in," Sky's team boss told BBC Sport. "I'm not going to lie, contrary to popular opinion I have got some emotions."
He gave the OK to a nine-man team that did not include the 2012 winner but one built around Sky's 2013 winner, Chris Froome. Froome can count on Richie Porte, David Lopez, Mikel Nieve, Vasil Kiryienka, Danny Pate, Geraint Thomas, Xabier Zandio and Bernhard Eisel.
Wiggins raced last with Froome at the World Championships in Florence and followed a different programme since winning the 2012 title. This year, he placed ninth in Paris-Roubaix and won the Tour of California but did not seem to be on the Tour de France path when he skipped both the team's altitude camps in Tenerife.
Brailsford confirmed his exclusion last Friday and left Wiggins to race the Commonwealth Games in Glasgow and possibly the Vuelta a España. He explained that he had to put his emotions aside when selecting the nine.
"Of course it's difficult. It's a challenging one, because on the one hand I've got to do my job and think about how to win," Brailsford said.
"You take all the emotion out of it and you look at the logic and you figure out what it's going to take to win. I've done that for a long time now and it's stood us in very good stead. We've dominated two Olympic Games with that mentality, we've won two Tour de France's with that mentality and I'm not going to change now."
Brailsford met Wiggins at a young age, worked with him on the track and helped him to gold medals in the Olympics. On the other hand, he only seriously began helping Froome when the team signed him from Barloworld for its 2010 debut season.
Over the last three seasons, Froome has proven Sky's golden ticket. He placed second to Wiggins in 2012. In 2013, he won most of the stage races he participated in en route to the Tour title. This year has been rockier for the Kenya-born Brit, but still convincing enough to allow him absolute leadership when the race departs from Sky's backyard on Saturday.
"It was a very, very difficult decision. But ultimately I've got to stick with what got us to this point in time," Brailsford added.
"From a performance point of view, from a professional point of view it's straightforward, but from a personal point of view it kept me awake at night, that's for sure."
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