The 33-year-old - who had been linked with a third spell with Rangers - has signed a deal that will tie him to the Major League Soccer club until June 2014.
The former Celtic and Hibernian striker, who was this week named in the Scotland squad to face England at Wembley next month, has scored six goals in 11 starts this season after an injury-affected debut campaign in Canada.
Miller told his club's official website: "I'm delighted to sign a contract extension with the Whitecaps. I've really enjoyed my time in Vancouver and so has my family.
"The fans here are unbelievable, the club is always very professional, and I think we have a special group of players."
Head coach Martin Rennie added: "Kenny is a great leader and his contributions both on and off the pitch have been instrumental to the success of our team."