Jordan Harvey had Vancouver's first goal in the 14th minute in front of a sellout crowd of 21,000 at B.C. Place Stadium. The Whitecaps improved to 2-0-2.
''I don't think you could ask for much more (to start the season),'' Miller said.
Miller rolled his spot kick into the right corner of the net, lifting the Whitecaps to a 2-0 lead. Ricardo Clark responded for Houston in the 75th minute, but that was all the scoring for the Dynamo (2-1-0).
Miller had to re-take his crucial kick because teammate Darren Mattocks was still in the 18-yard box when he put the ball into the net.
''It was a little tougher when you've scored the first one, and it's easy after a miss,'' Miller said. ''But sometimes that happens. It was a little bit of encroachment there. Sometimes, the referees don't make you take it again. But I was fortunate enough to put it in.''
The penalty kick was awarded after Houston defender Kofi Sarkodie was called for a hand ball in the box in the 56th minute.
Harvey gave the Whitecaps a 1-0 lead when he bounced Andy O'Brien's header past Dynamo goalkeeper Tally Hall. The play originated off a long cross from the left flank by Pedro Morales.
The assist was the first MLS point for O'Brien, who joined the Whitecaps midway through the 2012 season. Harvey's goal came two minutes after Mattocks volleyed a Miller cross just over the crossbar.
''I like to think I can contribute, not just with assists and things like that,'' O'Brien said. ''But I'm pleased that I could contribute on the goal.''
After assisting on the goal, O'Brien made several timely defensive plays.