Wide receiver Quinton Patton, who was inactive for the first 13 games, had touched the ball just two times this season before he fumbled in overtime Saturday after a 20-yard run on an end around.

So why were the 49ers turning to Patton at a critical point in their 38-35 overtime loss to San Diego? They were running out of options.

Patton and Anquan Boldin were the only healthy wide receivers remaining: Stevie Johnson (knee) was inactive and Bruce Ellington (hamstring) and Brandon Lloyd (hip) exited early. That forced Michael Crabtree to return to the game with a knee injury that limited him in practice during the week. Crabtree played 15 snaps and his only catch, a 5-yarder, came on the first play of overtime.

In addition, running back Frank Gore, 31, already had 26 carries, his most since 2011, with his backup, Carlos Hyde, inactive because of an ankle injury.

The storm of injuries likely led the 49ers to hand the ball to Patton on a play they’ve used with Ellington, who had three carries before he was injured Saturday.

“I was just trying to make a play,” Patton said. “They chose to give me the ball, and I wanted to make a play. The ball came out. I didn’t get it in tight enough like I am coached to do. I let the ball hang out a little bit.”

More injuries: The attrition wasn’t limited to the offense.

Michael Macor / The Chronicle

The defense, which has placed seven players on injured reserve during the regular season, continued to be ravaged by injuries.

Most notably, safety Eric Reid left in the first quarter after sustaining the third concussion of his two-year career. Reid had two concussions in a two-month span in 2013, but didn’t miss a game.

Cornerback Leon McFadden also sustained a concussion, and outside linebacker Aldon Smith (head), cornerback Perrish Cox (undisclosed) and outside linebacker Aaron Lynch (ankle) all returned to the game after they were sidelined.

Smith was being evaluated for a possible concussion when the Chargers scored the game-tying touchdown on Philip Rivers’ 11-yard toss to Malcom Floyd with 29 seconds left.

Because of injuries, the 49ers had four starters Saturday — Lynch, nose tackle Quinton Dial, defensive tackle Tony Jerod-Eddie and inside linebacker Nick Moody — who entered with a combined nine career starts.

Run to defeat: The 49ers had a franchise-record 355 rushing yards, which was the most in the NFL since 2007 and the 24th-highest total since 1940.

What made it unique? It came in a loss: The top 23 rushing performances in the past 74 years came in victories.

In fact, there have been 32 rushing performances of 350 yards since 1940 and only one other came in a defeat: The Chiefs ran for 352 yards in a 20-13 loss to the Colts on Dec. 23, 2012.

Dynamic duo: Gore (158 yards) and Colin Kaepernick (151) became the fourth pair of teammates — and the first since 1976 — to have 150-plus rushing yards in a game. The last tandem to do so was the 49ers’ Wilbur Jackson (156) and Delvin Williams (153) in a 20-16 win over the Vikings on Nov. 29, 1976.

Kaepernick, who has the top two postseason rushing performances by a quarterback in NFL history, had the third-highest regular-season total by a QB.

In addition, Kaepernick’s 90-yard touchdown run in the third quarter was the second-longest by a quarterback in NFL history behind a 93-yard score by Oakland’s Terrelle Pryor on Oct. 27, 2013.

Briefly: The 49ers had three plays gain 25-plus yards, two more than they had in their previous three games. … Gore needs 38 yards in the regular-season finale against the Cardinals to become the 11th running back in NFL history with eight 1,000-yard seasons. He needs 39 yards to pass Warrick Dunn (10,967 yards) for 20th on the NFL’s all-time rushing list. ... The 49ers are 3-4 at Levi’s Stadium. They were 21-4-1 in their last 26 regular-season games at Candlestick Park.

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