Morse will receive salaries of $3.25 million in 2012, and $6.75 million in 2013.
He also gets a signing bonus of $500,000.
The Nationals announced Friday they had reached a deal with Morse before arbitration figures were exchanged this week, but it was contingent on his completing a physical exam, which he's now done.
The 29-year-old Morse, who also plays first base, hit for a .303 average with 31 homers and 95 RBIs in 2011 -- leading the Nationals in each category.
He has spent seven seasons in the majors with the Nationals and Seattle Mariners, but really emerged over the last two years as a regular in Washington. Of his 52 career homers and 183 RBIs, 46 homers and 136 RBIs came in the 244 games Morse played in 2010-11.