With the score tied 1-1 in the eighth, John Baker led off with a single against Nationals starter Jordan Zimmermann and was eliminated at second on pinch-hitter Amarista's groundout.
Amarista then advanced to second on Zimmermann's errant pick-off throw and came home with the decisive run on Everth's RBI hit.
The late run made a winner of Eric Stults (4-3), who yielded just one run on four hits over eight innings. The left-hander walked two and struck out five.
Huston Street notched his 10th save despite issuing two walks in the ninth as the Padres took their first win in a four-game series against the Nats.
Yonder Alonso went 2-for-3 with a solo homer for the victors.
Zimmermann (7-2) absorbed the complete-game loss, allowing just one earned run on seven hits. He didn't issue a walk and fanned six.
Steve Lombardozzi got Washington's only RBI.