The same problem landed the 32-year-old right-hander on the disabled list for the second time this season from Aug. 16 through Sept. 5.
Right-hander Carlos Monasterios will start on Sunday for the Dodgers against Nelson Figueroa.
When asked if Padilla was out for the season, Dodgers manager Joe Torre said, "It wouldn't surprise me."
On Thursday, Padilla threw a bullpen session and reported no problems. On Friday, Padilla threw on flat ground and said he felt fine physically.
"But later it started bothering him and he told me about the fifth or sixth inning [Friday] night," said head trainer Stan Conte. "[Saturday] he came in a little worse. That predicated to us knowing he wouldn't pitch [Sunday].
"We're assuming that it's a recurrence of the disc bulge that's irritated. Based on what he told me last night, obviously he can't pitch."
Conte said most people that have a disc problem in the neck have pain down the arm. Padilla has pain in the middle of his shoulder blade on the left side.
Padilla had an extended stay on the DL from April 23-June 19 with an inflamed radial nerve in his right arm. On Monday at San Diego, Padilla made his first start since Aug. 15 at Atlanta and allowed three runs in four innings in the Dodgers' 4-2 loss. He gave up five hits with one walk and five strikeouts over 59 pitches.