Marquis (7-2) picked up right where he left off last Sunday at San Francisco where he shut out the Giants through 5 2-3 innings before he was ejected for hitting Justin Upton with a pitch.
He was suspended for five games and fined him an undisclosed amount. But he appealed the suspension and fine, and is able to pitch until there is a decision on his appeal.
Morse staked Marquis to a lead with a two-run homer off Mat Latos (4-7) in the second inning. Lance Nix led off with single, then Morse hit a 1-2 fastball into the left-field seats for his 10th home run.
Morse has homered eight times in his last 18 games.
Tyler Clippard pitched two hitless innings and Drew Storen worked the ninth for his 13th save in 14 chances to complete the combined four-hitter.
Two of the hits came after Morse’s homer.
The Padres loaded the bases in the sixth on Chris Denoria’s one-out double, a single by Jason Bartlett and a walk to Brad Hawpe. Ludwick drew a full-count walk to bring home one run.
That brought up Anthony Rizzo, the Padres‘ prized prospect who made his highly anticipated major-league debut Thursday night. After running the count to 3-2, Marquis struck out the rookie. He then got Jose Cantu to end the inning with a groundout.
Rizzo finished 0 for 1 with a strikeout, two walks and was hit by a pitch. In two games, Rizzo is 1 for 3 with four walks, one run scored, one hit by pitch and two strikeouts. The first baseman committed a fielding error in the ninth inning on a ground ball.
Latos, who won his previous three starts, gave up two runs and four hits, struck out a six and walked two.
San Diego, which had won nine of 13 games, dropped to an NL-worst 14-24 at home. The Nationals won for just the third time in eight games.