Willingham will have surgery in Washington early next week to fix the problem and will miss the remainder of the season. He has been dealing with knee issues since April, but the problem grew worse recently.
After Sunday's game, in which he collected two hits against the D-backs, Willingham's knee started to bother him. It grew worse when he flew back to Alabama to be with his family on Monday.
The pain didn't subside once he arrived in Atlanta on Tuesday. He was hitting .268 with 16 homers and 56 RBIs when he was placed on the disabled list. Willingham was not available for comment on Thursday.
"It's a tough blow for him personally," Nationals manager Jim Riggleman said. "He is such a pro. He likes to play. He is out there pretty much every day. He did a good job. For the ballclub, it's tough to fill out the lineup without him in there because he is good protection for Adam Dunn."
With Willingham out for the season, Roger Bernadina will get most of the playing time in left field, with Morgan in center and Mike Morse and Willie Harris platooning in right field. Bernadina has played most of the season in right field.
"I was always told that left field was Roger's best position. I've seen him out there a little bit," Riggleman said.
As for the lineup, Dunn will bat third with Ryan Zimmerman hitting fourth. Who will give Zimmerman protection is not known. Bernadina or Morse could be the guy.
"There is a lot of things that go into it," Riggleman said. "But we are going to try to have them get some pitches to hit -- one way or the other.
Morgan, who had been recovering from a right hip flexor strain, played two rehab games recently and took batting practice with the Nationals on Wednesday. The 30-year-old center fielder was batting .261 with 20 RBIs and 29 stolen bases entering Thursday's game.