With runners at the corners and two outs, Adam Jones hit a grounder to Scutaro, whose throw to second on an attempted force-out sailed past Jed Lowrie and down the right field line, allowing Brian Roberts and Luke Scott to score to make it 3-0 Baltimore.
Scott and Felix Pie homered in the eighth inning and the O's took the first of a three-game series against Red Sox at Camden Yards.
Brian Matusz (7-12) limited Boston to two runs on six hits over six frames, walking one and striking out six.
Josh Beckett (4-4) allowed two earned runs in on seven hits in seven innings of work for the Red Sox, who fell to eight games out of first in the American League East.
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