Shoppach, 33, will report to Triple-A Syracuse.
A nine-year major league veteran, Shoppach played 35 games with the Mariners this season, posting a slash line of .196/.293/.346 with three home runs and nine RBIs in 107 at-bats.
Shoppach's best offensive season came in 2008, when he hit .261/.348/.517 with 21 homers and 55 RBIs with the Indians.
Considered a solid defensive catcher with a good arm, Shoppach threw out 37 percent of attempted base stealers this season (10-of-27).
The Nationals will be Shoppach's fifth organization in the last three seasons.