The Orioles had a 5-3 lead going into the seventh and Mark Hendrickson (1-5) came out for his second inning of work.
Hendrickson, however, gave up a leadoff single to Darnell McDonald and Scutaro blasted a one-out, two-run homer that tied it. J.D. Drew then drew a walk and scored the go-ahead run on a double by Victor Martinez.
David Ortiz was then walked intentionally, bringing up Beltre, who hit an 0-1 pitch over the wall in left for a three-run homer.
Jon Lester (15-8) got the win, although he gave up five runs on eight hits in six innings. Jonathan Papelbon worked a 1-2-3 ninth for his 34th save.
Baltimore had a four-game winning streak snapped.