Quintana, who rides for the Movistar team, beat compatriot Rigoberto Uran by two minutes and 58 seconds overall.
“I’ve learnt to overcome adversity and to manage a team over three weeks, to be a leader,” Quintana said. “It’s really emotional.”
Meanwhile, Britain’s Geraint Thomas won the 2014 Bayern Rundfahrt, after his victory in the same competition back in 2011.
“This win has definitely boosted my confidence heading into a busy summer,” the Welshman said.