"He wanted to [play], but we wanted to stay a bit on the cautious side," Giants manager Bruce Bochy said after the Giants' 9-2 loss, adding that Pagan should be fit to play in Friday's Interleague series opener at Detroit.
Juan Perez replaced Pagan in center field, batting eighth. Left fielder Gregor Blanco moved into the leadoff spot.
Third baseman Pablo Sandoval was the other Giants regular not to start against the Rockies. Bochy wanted to give Sandoval what amounted to a two-day rest, combined with Thursday's scheduled off-day.
"He needs a day [off]," Bochy said of Sandoval, who entered Wednesday having appeared in 135 of San Francisco's 139 games. "He's a little worn down."