SANTA CLARA, Calif. – After 49ers receiver Deebo Samuel took a pitch to the right for a 20-yard touchdown run down the sideline, Vikings head coach Mike Zimmer spent the ensuing television timeout chewing the ear of referee Brad Rogers.

Zimmer wanted to know why 49ers tight end George Kittle wasn't called for holding Vikings linebacker Eric Kendricks, who was the closest defender to Samuel before he turned the corner for the first of San Francisco's three rushing touchdowns in its 34-26 win.

"Most of the day," Zimmer said, "that's what I was talking to [officials] about."

Zimmer lamented officiating as his defense was already fighting attrition, playing without four defensive line starters after Dalvin Tomlinson was placed on the reserve/COVID-19 list and Everson Griffen was hospitalized to undergo mental health treatment this week. Defensive end Danielle Hunter and nose tackle Michael Pierce are on injured reserve.

So second-year defensive tackle James Lynch made his first NFL start. Newly acquired defensive end Tashawn Bower, re-signed off the Patriots practice squad midweek, was the first edge rusher off the bench behind Sheldon Richardson and D.J. Wonnum.

Eventually, the weathered floodgates broke as the 49ers racked up 208 rushing yards — 95 of which came during San Francisco's 21 unanswered points that put the Vikings in a 28-14 hole.

San Francisco running back Elijah Mitchell chipped away, finishing with 133 rushing yards despite none of his 27 carries g than 15 yards.

"It was a physical game," Kendricks said. "Refs let us play. Hats off to them, I respect them. They came with it and we knew their run game was really good; very complex, very confusing."

The Bay Area has been an unfriendly setting for Zimmer's run defenses, which surrendered 230 and 186 rushing yards in their previous trips in 2015 and the 2019 playoffs. But they haven't been as depleted on the defensive line as they were Sunday, when 49ers head coach Kyle Shanahan called six straight runs at the end of the one-score game to set up a field goal try.

"It was difficult," Zimmer said. "We had some guys that came in, I guess it was Wednesday, that played in the game. We had to move a tackle to end and things like that, so, but that's NFL life."

Coaches were forced to adjust the pass rush without Griffen, sometimes deploying three-lineman fronts with linebacker Anthony Barr as a fourth rusher. Before exiting with a hamstring injury, Barr had an early pressure that led to a sack by Wonnum.

Only one reinforcement, Tomlinson, could possibly return for next week's game in Detroit. Nose tackle Michael Pierce is technically eligible to come off injured reserve this week, but he's practiced just once since exiting the Oct. 3 loss to the Browns with an elbow injury.

"It's very tough," Kendricks said. "They played their hearts out today. Got a lot of respect for those people on defense. That game was not easy, and we fought. It sucks losing, sucks getting ran on like that. But it's inspiring, the guys are working hard, stepping up, studying."