The 33-year old Scottish striker has penned a six-month extension on his Designated Player deal which will keep him at BC Place until June 2014.
"This is an important move for our club and speaks to the value we place on continuity as we grow," said Vancouver head coach Martin Rennie in a club statement.
"Kenny is a great leader and his contributions both on and off the pitch have been instrumental to the success of our team. It's an exciting time for the club and we look forward to a strong finish to the 2013 campaign."
Miller, who has scored six goals in 12 MLS matches this season, added: "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."