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SANTA CLARA — The San Francisco 49ers have made it clear to the rest of the NFL that they can stop the run. But can they stop a top-flight passer?

The 49ers get another opportunity Sunday to show what they can do against a top quarterback when Eli Manning and the New York Giants come to town for a showdown of NFC division leaders.

San Francisco faced two challenging quarterbacks earlier this season — and struggled against each. The 49ers allowed a combined 761 yards and four touchdowns passing to Dallas' Tony Romo and Philadelphia's Michael Vick. Those are San Francisco's two closest games of the season, and the game against Dallas was the Niners' only loss.

But the 49ers have improved against the pass since then, making a defense that ranks No. 1 in the NFL against the run even stronger.

Manning could present the stiffest test for that unit since Vick threw for a career-high 416 yards against the 49ers on Oct. 2 during San Francisco's 24-23 victory. That comeback win was the springboard to a 7-1 start that has the 49ers leading the NFC West by five games at midseason.

"A lot of teams have abandoned the run on us and went to an aerial attack," 49ers strong safety Donte Whitner said Friday. "When it comes down to crunch time and getting in the playoffs, and playing these other top teams in the NFC, you have to stop elite quarterbacks to get to where we want to go. This is just another step to show that we've made a lot of improvement."

The 49ers rank 22nd in the NFL in pass defense, but they have allowed an average of only 245.5 yards through the air since the Philadelphia game.

Meanwhile, their rush defense has just gotten tougher. San Francisco has allowed an average of 61.3 yards on the ground in its last three games, leaving opponents few alternatives but to test the Niners on the back end.

Manning has played a key role in New York's 6-2 start, leading the Giants to four fourth-quarter comeback victories this season.

"He's a quarterback that's been there, that's played at the highest stages, that's played in a lot of big games," free safety Dashon Goldson said. "They have a good quarterback and good wide receiver corps and it's going to be another challenge and an opportunity for us to show what we can do. I think we're up for the challenge."

San Francisco's secondary has played better since Goldson returned to the starting lineup after missing the season's first two games with a knee injury. That included the 27-24 overtime loss against Dallas, when Romo and Jon Kitna combined to riddle the 49ers for 432 yards passing.

Goldson is the only member of San Francisco's starting secondary to start a game for the 49ers last year. Whitner and left cornerback Carlos Rogers joined the team in August as free agents, and holdover veteran Tarell Brown won the starting job at right cornerback during the summer.

It took a while for the unit to come together. But now it is regularly making plays like the rest of San Francisco's opportunistic defense.

Linebackers Patrick Willis and NaVorro Bowman are among the NFL's leading tacklers, but they also play on passing downs and have been strong in underneath coverage against tight ends and running backs. Bowman has noticed the improvement in coverage by the secondary behind him.

"It's those guys just being honest," Bowman said. "Everybody wants to get there in the box and make a play against the run. But we've been having success with a seven-man box and giving our secondary a chance just to play the pass and focus on that. Those guys have just been doing a great job of recognizing the pass and defending it. With us playing a Pro Bowl quarterback this week, I think they'll be focusing more on that than trying to stop the run."

The 49ers have 10 interceptions and lead the NFL with 60 passes defensed through eight games.