Jones (3-for-4) delivered his homer in the third inning and Markakis followed with his shot in the fifth, staking the Orioles to a 6-0 lead.
Robert Andino contributed a two-run single among his two hits for the American League East-leading Orioles, who posted their fifth straight win and seventh victory in nine contests overall.
Jason Hammel (5-1) got the win despite yielding four runs on six hits over 5 1/3 innings.
Steve Lombardozzi and Bernadina each finished with two hits and an RBI for the Nationals, who dropped their third straight.
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