The visitors did take the lead minutes later when Brown was hauled down by Eric Avila and the referee pointed to the spot. The striker made no mistake in sending Kennedy the wrong way.
Atiba Harris could have give the Rapids a two-goal lead but his powerful effort from the edge of the area was beaten away by Kennedy.
Chivas had a great opportunity to get level when they were awarded a penalty of their own when Jose Correa was pushed by Shane O'Neill. However, Correa blasted his kick off the bar and the ball was cleared.
After the break, substitute Laurent Courtois almost got the home side on level terms but he lost his composure at the last minute when bearing down on goal and sliced his effort over.
Brown almost made sure of the points for Colorado late on but after rounding Kennedy, he couldn't direct his shot goalwards. However, the Rapids still held out for the win.