SANTA CLARA -- A season-high 11 penalties rained down on the 49ers in their last game. It was the second time in a month that they'd been flagged 10 times or more.

Physicality, not dirty play, had been a trademark under coach Jim Harbaugh, who wants this penalty trend to end Sunday against the Miami Dolphins at Candlestick Park.

"That's not the way we want to play," Harbaugh said of a team that is the fourth-most penalized in the NFL. "That's not the 49er way of playing football."

The penalties have spoiled many a 49ers offensive drive and extended those of the opposition. Such was the case when Dashon Goldson committed an unnecessary-roughness penalty Sunday that the Rams parlayed into an overtime-forcing field goal.

"Penalties are going to come, and guys try to pick on us," Goldson said. "We can't let it slow us down. We've got enough on our plate to worry about fines or referees."

Only three teams have committed more penalties than the 49ers' 88 (for 744 yards): the Washington Redskins, Dallas Cowboys and Rams, all with 97 penalties. The Ravens, coached by Harbaugh's older brother John, also have been penalized 88 times.

To put it in further perspective: The Raiders, despite their notorious history as penalty magnets, entered their Thursday game having been penalized 11 fewer times than the 49ers.

"That's something we really have to improve on, that's something that's really hurt drives," 49ers left tackle Joe Staley said.


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Staley's third holding penalty this season -- he had none a year ago -- wiped out a 16-yard run by Frank Gore in Sunday's second quarter.

Although Staley didn't argue the call upon reflection, Harbaugh questioned it, along with others that have thwarted drives.

"Some of them were really, really questionable, in our opinion," Harbaugh said.

"What can you do to correct it? Keep the hands inside. The hands were inside with Joe Staley."

That wasn't the most questionable call, however. Although Colin Kaepernick's third-quarter pass appeared to cross the line of scrimmage, officials saw otherwise and ordered an intentional-grounding penalty that produced a Rams safety.

C.J. Spillman committed a penalty on special teams, where this season he's racked up as many penalties as tackles (seven).

Guard Mike Iupati also has committed a team-high seven penalties, including his fourth holding call last week.

Nobody has racked up more penalty yards than Goldson's 87, which have come through unnecessary roughness (three), unsportsmanlike conduct (two) and pass interference (one).

Goldson's latest violation came when he hit Rams quarterback Sam Bradford, who was sliding at the end of an 11-yard run. The 15-yard penalty vaulted the Rams to the 49ers' 40-yard line, setting up Greg Zuerlein's 53-yard field goal that forced overtime.

Goldson didn't agree with the call at the time or even upon reviewing it on film later.

"He's got to do a better job sliding," Goldson said. "What if he fakes a slide? I was on my way (for the tackle). It could have gone either way."

Defensive coordinator Vic Fangio had a more stringent take, noting that Goldson or anyone else has to avoid sliding quarterbacks at all costs.

But Fangio isn't about to temper Goldson's aggressive nature: "You don't pull the reins back. You explain why the penalty was called and why you can't do what you do. He's smart enough to know the difference, and he just needs to remind himself."

Offensive coordinator Greg Roman needs no reminder about how drives have been spoiled by penalties, such as holding, false start and delay of game.

"That's something we've got to get a lasso around real quick," Roman said. "Forty-Niners football (is) smart, tough, opportunistic football. And penalties certainly don't fit into that equation."

For more on the 49ers, see Cam Inman's Hot Read blog at blogs.mercurynews.com/49ers. Follow him on Twitter at twitter.com/CamInman.