"It's been a rough spring. Time to hit the reset button," he wrote on his personal Twitter account on Friday afternoon.
The talented American is expected to now take a break before building up for the Tour de France, where he will the sole leader for BMC.
Van Garderen has battled through a roller coaster spring campaign. He started the season with an impressive second place at the Tour of Oman behind Chris Froome (Team Sky) but was forced to quit Paris-Nice on stage one due to illness. He bounced back to finish third overall at the Volta a Catalunya and win the decisive mountain stage to Vallter 2000-Setcases. He was sixth overall at the Vuelta al Pais Vasco and was targeting success at the Tour de Romandie but crashed hard in the prologue time trial.
He continued in the race despite racing in pain but opted to retire during Friday's mountain stage to avoid worsening his injuries.
"I had a pretty nasty crash in the prologue where I hit my hip pretty good. I had x-rays and there were no broken bones but it was pretty painful," van Garderen said in an interview published on the BMC team website.
"I was optimistic it was getting better each day and that I could finish the race up strong. But when we hit the steep climbs today (Friday), it really started aggravating and flaring up. I just thought it wasn't worth risking doing further damage by staying in the race. It is better to rest it and kind of turn the page on the spring and focus on the Tour de France, which is what is most important."
Van Garderen won the Tour of California in 2013 but will not return to the race this year after he and the BMC opted to focus on the Tour de France. He is expected to return to racing at the Critérium du Dauphiné, where he finished third overall in 2010.
"Tejay needs two or three days of nothing for a good recovery," BMC directeur sportif Yvon Ledanois said. "But I have confidence in him for his next races. This won't be a problem."