Left-hander Eric Stults will start in Stauffer's place on Saturday against the Angels at Petco Park. He reported to the club on Friday after the Padres claimed him off waivers from the White Sox.
Stauffer said he experienced soreness in his elbow -- in his flexor tendon bundle -- late in his outing on Monday. He allowed four runs (three earned) in five innings against the Nationals.
"Probably last inning, I can't think of one pitch in particular. When I came out it was pretty sore and it felt like it was fairly weak at that point," he said. "It was pretty sore there the next couple of days. I played catch and tried to let it go a little bit, and it didn't feel right."
Stauffer said he underwent an MRI exam on Friday but he had yet to receive the results.
"Obviously, it's very frustrating," said Stauffer, who was originally expected to be the Padres' Opening Day starter. "I'm just trying to get a handle on what's going on and what needs to be done."
Of the Padres' 12 players who are sidelined, four are on the 60-day DL.
"I would speculate this is by far the most I've seen at any one time so early in the season," Padres manager Bud Black said about his club's rash of injuries.
Combined, they had missed 275 games entering Friday's game against the Angels.
"It's an organization challenge," Black said. "It's a roster challenge for [general manager] Josh [Byrnes], because you're seeing new guys come in out of the organization, Josh having to juggle the 40-man roster and a lot of it has been done via the 60-day disabled list."
Stauffer said he felt fine during his three rehabilitation starts before he made his 2012 debut. He went 0-1 with a 1.72 ERA during those outings -- two rehab starts with Class A Lake Elsinore and one start with Triple-A Tucson.
"The rehab starts, I felt good through there," Stauffer said. "I don't know if it's when the pitch count gets up there. I'm not sure exactly what the reasoning is. It's the same sort of progression that happened earlier."
As for Stauffer's replacement, Stults allowed two runs in 6 2/3 innings in two appearances, including one start, for the White Sox this season. He is 8-10 with a 4.84 ERA in 43 games, including 25 starts, over parts of six Major League seasons with the Dodgers, Rockies and White Sox.
As for Darnell, he suffered his shoulder injury attempting to make a leaping catch on a Tony Gwynn liner to lead off the sixth inning in Thursday's 8-1 loss to the Dodgers at Petco Park.
Darnell said he was scheduled for an MRI exam on Friday night.
"It's too hard to tell at this stage," Darnell said. "Even the doctor, when he looked at me, he doesn't even know. He can't really guess or predict [before the MRI]. [The shoulder is] just sore."
Darnell said the injury is different from an injury he suffered last year on the same shoulder. He underwent season-ending arthroscopic surgery on Sept. 20 to stabilize the strained left shoulder.