Per club policy, terms of the contracts were not disclosed.
"Peter is an experienced MLS player that reads the game well and is strong technically," said Whitecaps FC head coach Teitur Thordarson. "He will bring additional leadership to our squad, as we head into an important stretch of our season."
Vagenas was drafted by the Galaxy in the second round of the 2000 MLS SuperDraft following a successful NCAA Division I career at the University of California, Los Angeles (UCLA).
"I'm very pleased to join Vancouver Whitecaps FC," said Vagenas. "I've played in this league for a number of years and I've had some great experiences playing with the Galaxy and Sounders FC. I'm excited to start this new challenge in Vancouver."