The Giants had been trailing 1-0 since in the third but broke through to grab the lead in the sixth.
One out later, Brandon Belt delivered a ground-rule double, sending Scutaro to third, and after Buster Posey was intentionally walked, Pence struck a two-bagger, scoring both runners.
Guillermo Moscoso (1-0) earned the win with two innings of scoreless relief and Sergio Romo picked up his 28th save as the Giants bounced back from a 5-2 loss in Friday's three-game series opener.
Chen (6-5) was touched for three runs on five hits over six innings.
Chris Davis belted his MLB-leading 42nd homer for the Orioles.