SEATTLE — A fourth-quarter roughing-the-passer penalty hurt the 49ers far more than Seattle quarterback Russell Wilson did.

In the 49ers’ estimation, the Seahawks’ second touchdown in their 17-7 win Sunday came with gift wrapping. With his team leading 10-7 in the fourth quarter, Wilson threw an incompletion on a 3rd-and-5 at the 49ers’ 15-yard line while being pressured by safety Antoine Bethea and linebacker Nick Moody, who was flagged for roughing on what appeared to be a clean hit.

Two plays later, Wilson threw a 10-yard touchdown to Paul Richardson with 13:20 left to finish the scoring.

San Francisco head coach Jim Harbaugh, who was livid on the sideline, said after the game that he disagreed with the call, and that sentiment was echoed in the locker room.

“I think it was a bad call,” Bethea said. “It’s so up and down with those type of calls. One week, you see something, another week, you see another. … It was a tough call, crucial moment on third down.”

Said referee Ed Hochuli: “I felt that (Moody) hit the quarterback in the chest with the (crown of his helmet) and that’s a foul unless he has his face completely up. … It’s a foul. That’s why I called it.”

Injury report: Three starters — right tackle Anthony Davis, center Marcus Martin and cornerback Chris Culliver — were inactive because of injuries, and five more players didn’t finish the game: running backs Frank Gore (concussion) and Carlos Hyde (knee), inside linebacker Chris Borland (ankle), outside linebacker Ahmad Brooks (thumb) and tight end Garrett Celek (ankle).

In the locker room, Borland was in a walking boot and Brooks’ thumb was heavily bandaged. Hyde, whose body was bent back awkwardly in the third quarter, insisted his injury was minor.

“It wasn’t as bad as it looked,” he said. “I’ll be back next week.”

Seattle head coach Pete Carroll acknowledged that Borland’s injury on the final play of the second quarter could have set the stage for the Seahawks’ second-half success. The Seahawks had 105 of their 152 rushing yards after Borland was replaced by Moody, who didn’t play a defensive snap in the first 13 games.

“I don’t know the other guy (who) came in,” Carroll said. “I don’t know how much he’s been playing — I haven’t seen him much. Borland’s been playing great football. We knew that he was out, and that just added to the fact that we were going to run the football, anyway. He is such a good player that he makes a difference.”

Dud for Davis: After saying four days before kickoff that he is a “playmaker” who wants to be more involved in the passing game, tight end Vernon Davis didn’t get his wish.

His stat line: two targets, no catches.

It was the latest disappearing act for Davis against the Seahawks. In his past seven meetings against Seattle, he has 10 catches for 97 yards and a touchdown.

Davis had company. The 49ers’ wide receivers combined for six catches for 54 yards. Fullback Bruce Miller led the team in receptions (four) and receiving yards (56), and Celek had the longest catch (31 yards).

Eric Branch is a San Francisco Chronicle staff writer.