Missing two stars, 49ers defense is still excelling

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Five games into the season, the 49ers rank among the NFL’s top five in a slew of defensive categories: yards allowed per game (second), rushing yards allowed per game (third), takeaways (fourth) and opponent’s passer rating (fourth).

Given those figures, it’s fair to wonder: What could they accomplish when two of the league’s best players are on the field?

Of course, Vic Fangio is eager to have All-Pro linebackers Aldon Smith and NaVorro Bowman back in the lineup, but the 49ers’ defensive coordinator will exercise patience waiting for Bowman to come back from a severe knee injury suffered in the NFC Championship Game fewer than nine months ago.

Bowman, who is on the physically unable to perform list, is eligible to return to practice next week. However, Fangio suggested that Bowman won’t be back on the field that soon. He can return to practice at any point from Oct. 14 to Nov. 24. Once he starts practicing, the 49ers have a three-week window during which they can place him on the 53-man roster.

“I think at some point, he’ll eventually play” this season, Fangio said Tuesday on KNBR.

Fangio said Bowman had had no “roadblocks” in his rehabilitation and is ahead of schedule in his recovery. Once he starts practicing, the 49ers could utilize the full three-week practice window before activating him from the PUP list.

Meanwhile, Smith’s return date isn’t muddled. He is serving a nine-game suspension and is on track to play on Nov. 16 when the 49ers visit the New York Giants. Smith can’t practice with the team during his suspension, but he’s been taking advantage of his ability to work out at the facility.

“He said, 'I’m the most fit guy in this building,’” Fangio said. “He seems to be doing well along those lines, and we’re looking forward to his return here down the line.”

Justin Smith sacks the Bears' Jay Cutler in a game where the defense had a rare failure this season. Justin Smith sacks the Bears' Jay Cutler in a game where the defense had a rare failure this season. Photo: Scott Strazzante / The Chronicle Photo: Scott Strazzante / The Chronicle Image 1 of / 3 Caption Close Missing two stars, 49ers defense is still excelling 1 / 3 Back to Gallery

In the meantime, the 49ers hope their replacements continue to shine.

On Sept. 28, they held the Eagles’ offense scoreless in a 26-21 win and didn’t allow Philadelphia to cross its own 43-yard line in the first 55 minutes. Sunday, they held the Chiefs to no points, one first down and 37 yards in the final 26-plus minutes of a 22-17 victory.

Since the first quarter of the regular-season opener, the 49ers have played without four projected defensive starters: Smith, Bowman, nose tackle Glenn Dorsey (biceps) and cornerback Tramaine Brock (toe).

Dan Skuta and Michael Wilhoite, two former undrafted free agents from Division II schools, have assumed Smith’s and Bowman’s spots in the starting lineup. Nose tackle Ian Williams, who opened 2013 as a starter before suffering a season-ending ankle injury in Week 2, has replaced Dorsey, who is eligible to return as early as Nov. 9 against the Saints.

Brock, who was injured in Week 1, has been replaced by Perrish Cox, who has starred in the secondary. Cox is tied for the NFL lead in interceptions (three) and fumble recoveries (two) and ranks first in passes defended (10).

“He’s done well,” Fangio said. “And he’s somewhat a prophet, too. He told me before (last week’s) game on the field he was going to get a pick and give me the ball. And he saved it for the right time.”

Indeed, Cox had a game-sealing interception for the second straight week, picking off Alex Smith on Kansas City’s final drive with two minutes left.

Ventrone back: With their coverage units both ranked in the bottom half of the NFL, the 49ers re-signed special-teams standout Bubba Ventrone, a source said.

Ventrone, 31, was among their final roster cuts Aug. 30 despite ranking third in special-teams tackles (15) last year for a team that ranked fifth in kickoff coverage (20.4 yards per return) and 13th in punts (8.7). The 49ers brought Ventrone back with their punt-coverage unit ranked 31st in the NFL (14.8 yards per return) and their kickoff-coverage team ranked 20th (23.9).

The 49ers haven’t announced which player they’ll release to make room for Ventrone on the 53-man roster.

Roster move: The 49ers signed guard Andrew Tiller, 25, to the practice squad and waived offensive tackle John Fullington. Tiller, a 2012 sixth-round pick of the Saints, has spent time on the Chargers’ and Packers’ practice squads.

Eric Branch is a San Francisco Chronicle staff writer. E-mail: ebranch@sfchronicle.com Twitter: @Eric_Branch