The 29-year-old Van Avermaet, was linked to Dr Chris Mertens, who is being investigated for providing ozone therapy to athletes, said he was relieved after hearing the decision.
"I am happy this nightmare is over," Van Avermae said. "This has been a hard period for me. Finally, I can focus only on cycling. I want to thank my friends, family and the BMC Racing Team, who supported me."
He was also accused of taking cortisone and Vaminolact, and was facing a two-year suspension, but his defence was able to prove that he had a prescription for the former and had not in fact used the latter.
BMC Racing Team President and General Manager Jim Ochowicz said the acquittal vindicated the team's decision to allow Van Avermaet to compete while an outcome in the case was reached.
"We never doubted Greg's innocence," Ochowicz said. "We are pleased with the decision."