Troy Tulowitzki also added a solo shot for the Rockies, who have hit seven homers in two nights against the Giants.
Morales (2-1) was masterful on the mound as he allowed five hits over seven innings, which matches the longest outing of his career. The left-hander's only mistake was a hanging slider to Hunter Pence in the fifth. It was Pence's second homer of the season.
LaTroy Hawkins got the final two outs in a rocky ninth for his sixth save in as many chances.