Colorado, which also took Tuesday's series opener, recorded the 18th win in its last 26 games at Olympic Stadium. The Rockies also improved to 8-3 under interim manager Clint Hurdle.
Chacon (3-4) scattered five hits and struck out two without a walk. But the 24-year-old righthander, who recorded his first road win of the season, left after six with a strained right pectoral muscle. He is listed as day-to-day.
Helton's two-out blast in the fourth off starter Carl Pavano (2-4) broke a scoreless deadlock. A former Expo, Walker hit his seventh homer of the season in the seventh, sparking a three-run burst and opening a 4-0 cushion for the Rockies.
Zeile padded the lead in the ninth with his seventh homer.
Rookie Brad Wilkerson had his second straight two-hit game for the Expos, whose season-high losing streak reached six games.