Lewis, a 12-time Pro Bowler, told The NFL Network during a pre-game interview that the injured toe on his right foot is still bothersome.
"There is a large amount of pain there, but I think it's more importantly about the injury," Lewis said. "Do I go ahead and re-injure it tonight on a very short week and fight it the entire rest of the season, instead of just going ahead and get through this stretch right now? The team is well prepared."
Lewis estimated that the toe felt about 85 percent healed, and he said that decision to sit came from the coaching staff.
Lewis called reports that the injury was of the season- or career-ending variety premature, saying, "I think all of those reports are terrible."
Lewis, whose consecutive starts streak ended at 57 when he was scratched prior to Sunday's victory over the Cincinnati Bengals, had practiced on a limited basis in each of the past three days. He had been listed as questionable in the team's final injury report on Wednesday.
Lewis' usual replacement also did not play. Dannell Ellerbe was deactivated after being limited the past three days by a balky hamstring.
Contrary to the pre-game report circulated in the stadium's press box, Albert McClellan — not Brendon Ayanbadejo — joined Jameel McClain as a starting inside linebacker. It was McClellan's first start of his career.
Defense gets after 49ers' Smith
After a few quiet weeks on the sack front, the Ravens defense got after San Francisco quarterback Alex Smith, collecting 9 sacks — which tied a team record for most in a single game.
The Ravens had recorded only four sacks in the previous three games.
The Ravens entered the game tied with the Philadelphia Eagles for fourth in the NFL with 29 sacks, but defensive coordinator Chuck Pagano had said Nov. 17 he deserved the blame for the underwhelming number of sacks in recent weeks.
"I've got to send them more," he said. "I've got to call more. That's not on them. That falls on my shoulders. I've got to be more aggressive and get after them."
49ers still stout vs. run
San Francisco demonstrated why it boasts the stingiest rush defense in the NFL.
The Ravens had a prime scoring opportunity with first down-and-goal from the 49ers' 4-yard line late in the second quarter, but could not get into the end zone, settling for a Billy Cundiff 23-yard field goal. The 49ers, who entered the contest as the league's top-ranked defense against the run (73.9-yard average) and had not permitted a 100-yard rusher in 32 consecutive games, are the only team in the NFL yet to allow a rushing touchdown.
"They haven't allowed any touchdowns, their yards per carry is really good. That's where they've been really good," quarterback Joe Flacco had said Tuesday. "And when they can do that, they can get after a pass or two."
Zbikowski gets first nod on kick returns again
As he did last Sunday, Tom Zbikowski got the first crack at returning kicks against the 49ers.
Zbikowski, who downed both of his opportunities, had said Wednesday that he was ready.
"You've just got to be prepared for anything and be prepared for everything," Zbikowski had said. "I'll go in there expecting to get some returns because I'd rather go into that way than not be prepared at all."
In addition to Lewis and Ellerbe, the Ravens deactivated cornerback Chris Carr (back), defensive tackle Arthur Jones (post-concussion symptoms), outside linebacker Sergio Kindle, rookie running back Anthony Allen (thigh) and wide receiver Tandon Doss. … Safety Haruki Nakamura (thigh), who had been upgraded from limited to full participation Wednesday and was listed as probable, was active. Wide receiver/kick returner David Reed was also active. He was scratched against the Bengals after fumbling three kick returns in his previous two contests. … The Ravens have now gone 19 consecutive games without surrendering a point on an opponent's opening possession. … The Ravens entered Thursday night's game with a 28-5 record when scoring first under coach John Harbaugh. Cundiff gave the team a 3-0 lead with a 39-yard field goal on the offense's first series. … For San Francisco, four starters — wide receivers Michael Crabtree (foot) and Braylon Edwards (knee), running back Frank Gore (knee) and right tackle Anthony Davis (ankle) — played Thursday night. … The 49ers deactivated guards Daniel Kilgore and Mike Person, fullback Bruce Miller, cornerback Shawntae Spencer, quarterback Scott Tolzien, wide receiver Brett Swain and nose tackle Ian Williams. … Free safety Ed Reed, left tackle Bryant McKinnie and punter Sam Koch represented the Ravens for the coin toss.