Hernandez allowed two runs in the third, another run in the fourth and gave up a solo home run to Xavier Nady and a single before being lifted in the fifth.
The Diamondbacks' lead in the National League West was cut to one game over the Padres and two over the Rockies. After Arizona concludes its series at Pittsburgh on Thursday, they head to Colorado for a three-game showdown.
"I don't know if we're pressing, trying to do too much," mused leadoff man Chris Young, who went hitless in the game. "We're just not getting the big hit right now. But we still have the lead, and it's not the worst thing in the world. We still control our own destiny. We've just got to win ballgames."
"It definitely puts some pressure on us, but you can't push the panic button," added cleanup hitter Conor Jackson, who drove in the Diamondbacks' sole run. "We're still in a good spot. We need to come out and play like we have the last two months. ... We're going to bounce back."
The Diamondbacks have lost five of their last seven road games, and have been outscored 18-7 in their last three games overall.