Beltre followed a two-run homer in the top of the sixth inning with an RBI single in a five-run seventh.
Catcher Jeff Clement had two hits, one a solo homer in the ninth. Ichiro Suzuki had five hits and scored twice and Beltre was the sixth player with two hits in an 18-hit attack for the Mariners, who swept the three-game inter-league series at Petco Park.
Winner Erik Bedard (5-4) gave up an earned run and just three hits before departing after 5 2/3 innings in favor of three relievers.
Edgar Gonzalez and Adrian Gonzalez drove in one run each for San Diego. Edgar Gonzalez and Scott Hairston had two hits apiece in the Padres' eighth loss in a row.
Losing pitcher Jake Peavy (5-5) surrendered three earned runs and 10 hits in six innings before the Padres' bullpen gave up the final six runs.