49ers’ defense: not damn good, but improving

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On Sunday, the 49ers made Chicago’s erratic quarterback, Jay Cutler, revert to Bad Jay.

A week earlier, they’d made Arizona’s Carson Palmer, an MVP candidate, look merely middling.

Cutler, who arrived with a 100.8 passer rating in his previous four starts, had a season-worst rating (64.2) in a 26-20 overtime loss to the 49ers. As for Palmer, he had a season-worst rating (80.4) and didn’t throw a touchdown pass for the only time in 12 starts in a 19-13 win over the 49ers on Nov. 29.

The recent evidence suggests the 49ers no longer find the zone-coverage concepts in defensive coordinator Eric Mangini’s system quite so confounding. On Monday, it was the first area head coach Jim Tomsula highlighted when asked about areas of improvement on his 4-8 team.

The 49ers have allowed two completions of 35-plus yards in their past four games after surrendering 13 such plays in their first eight games.

“Defensively, I will say that with the scheme, and the techniques, and playing together in some of the zone defenses — where the guys are and understanding where the other guys fit around you,” Tomsula said. “I think that’s an area that we’ve really improved.”

The 49ers have noted that Mangini’s system is more complex than that of former defensive coordinator Vic Fangio. A major difference: It features far more blitzing and zone coverage, where players cover certain areas of the field, as opposed to covering a specific player.

Chicago Bears running back Jeremy Langford (33) runs the ball against San Francisco 49ers safety Jaquiski Tartt (29) during the second half of an NFL football game, Sunday, Dec. 6, 2015, in Chicago. (AP Photo/Charles Rex Arbogast) less Chicago Bears running back Jeremy Langford (33) runs the ball against San Francisco 49ers safety Jaquiski Tartt (29) during the second half of an NFL football game, Sunday, Dec. 6, 2015, in Chicago. (AP ... more Photo: Charles Rex Arbogast, Associated Press Photo: Charles Rex Arbogast, Associated Press Image 1 of / 4 Caption Close 49ers’ defense: not damn good, but improving 1 / 4 Back to Gallery

In August, inside linebacker NaVorro Bowman insisted the 49ers would thrive in the scheme ... eventually.

“It requires you to do a lot of things when one person moves,” Bowman said. “That’s just something different that we haven’t been used to in years. But we’re putting the work in and (Mangini) is being really patient with us in learning the scheme ... But when we get it, we’ll be a damn good defense.”

Earlier in the season, the 49ers weren’t moving in sync. The 13 pass plays of 35-plus yards they allowed in their first eight games matched their total from the 2014 season.

Their confusion was impossible to miss. In a 43-18 loss at Pittsburgh in Week 2, inside linebacker Michael Wilhoite raised his hands in who-messed-up frustration after he ended up covering wide receiver Markus Wheaton deep downfield. The result of the mismatch: a 48-yard completion.

The following Sunday, in a 47-7 loss at Arizona, Bowman repeatedly mimicked Wilhoite’s exasperated gesture as receivers roamed free and Palmer threw for 302 yards and two touchdowns.

On Sunday, however, Bowman was clearly encouraged after another strong defensive performance. The 49ers, who haven’t allowed a passing touchdown in their past two games, had a 29-yard interception return for a touchdown from cornerback Jimmie Ward and limited Chicago to 20 points and 364 yards. (They had allowed 35.2 points and 464 yards in their previous five road games.)

The 49ers have allowed fewer than 365 yards in three of their past four games, a feat they managed twice in their first eight games.

“I really see that we can really have something special here,” Bowman said. “Maybe it didn’t come as fast as we wanted it, but we can definitely see the process. And it’s looking good for us.”

On Sunday, reasons for optimism included the performance of a host of young players in the secondary. Ward and cornerback Kenneth Acker, both 2014 draft picks, each received career-high grades from Pro Football Focus. In addition, promising rookie safety Jaquiski Tartt had a body-slam sack of Cutler.

Still, the defense has deficiencies. The 49ers have become better at limiting big plays, but they still aren’t making them. The 49ers rank 31st in the NFL in takeaways (nine), and Ward’s interception was their first forced turnover in 15 quarters. They also rank 20th in sacks (20) and have just six in their past five games.

Finally, despite their progress, they also aren’t far removed from allowing 510 yards and their most rushing yards (255) in 37 years in a 29-13 loss at Seattle on Nov. 22.

In other words, they’re still not damn good, but they’re moving in the right direction.

“I talked to the defense” Saturday, Bowman said. “… It was our job to get it right as quickly as possible, and I explained it was a process. We’ve built this process up to this point.”

Roster moves: The 49ers placed tight end Garrett Celek on season-ending injured reserve with a high ankle sprain he sustained Nov. 29. They re-signed inside linebacker Shayne Skov to fill Celek’s place on the roster.

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