LANDOVER, Md. -- A play from San Francisco 49ers head coach Kyle Shanahan's time with the Washington Redskins produced what proved to be the winning points against him on Sunday.

Kirk Cousins threw two touchdown passes and ran for another score on a read option as the Redskins defeated the 49ers 26-24 Sunday at FedEx Field.

After squandering all of a 17-0 lead, the Redskins scored nine fourth-quarter points on a field goal and a 7-yard run off a read-option by Cousins with 3:34 remaining.

"It's always going to be a part of our offense because it gives defenses something to think about," Cousins said of his former offensive coordinator.

"Kyle told me when he left, he said, 'I've learned after working with Robert (Griffin III) that this is a really valuable play no matter who the quarterback is. ...' When (head coach) Jay (Gruden) arrived we kept it and valued it. ... You've just got pick your spots, be smart with it, call it at the right time and you can get some yards."

Trailing 26-17, the 49ers answered on a 45-yard touchdown pass from rookie C.J. Beathard to wide receiver Aldrick Robinson with 1:58 left, but Washington recovered the onside kick.

The 49ers got the ball back with 52 seconds left, and got to the Washington 40. But an offensive pass interference call against wide receiver Pierre Garcon pushed them back to midfield, and Beathard's fourth-and-20 pass was intercepted with three seconds remaining, giving the 49ers their fifth straight loss by three points or less.

"It was a slant route on a flat route and the guy guarding the flat route ran into a guy," Shanahan said of the call on Garcon.

Washington (3-2) travels to Philadelphia a week from Monday to play the first-place Eagles (5-1), while the 49ers are 0-6 for the first time since 1979 in Bill Walsh's first season as head coach.

Cousins finished 25 of 37 for 330 yards and one interception. Running back Chris Thompson, starting in place of the injured Rob Kelley, gained only 33 yards on 16 carries, but had 105 yards on four receptions.

San Francisco quarterback Brian Hoyer was benched in the second quarter after completing 4 of 11 passes for 34 yards. Beathard came on to rally the 49ers and finished 19 of 36 for 245 yards, one touchdown, and the interception.

"He was cool, calm and collected like he'd been out there before," running back Carlos Hyde said of Beathard. "(He) went out there, went through his reads and did what he's supposed to do."

Shanahan said after the game that Beathard will remain the starter.

Hyde had a pair of 1-yard touchdown runs for San Francisco.

Robbie Gould's 52-yard field goal early in the third quarter pulled the 49ers within 17-10.

After a Redskins punt, Matt Ioannidis sacked Beathard for an 8-yard loss on third-and-5 and Gould missed a 47-yard field-goal attempt.

On the next play from scrimmage, however, Cousins' pass to tight end Vernon Davis was complete, but as Davis struggled for additional yardage, the ball popped out. Safety Jimmie Ward picked it up and ran 43 yards to the 1. Hyde scored on the next play and the 49ers had tied the score.

Washington responded with a 16-play drive that stalled inside the 5 before Dustin Hopkins' 21-yard field goal put the Redskins back in front 20-17 with 10:34 left.

On their next possession, the Redskins drove 84 yards in nine plays, with Cousins running for a score on the read option before Hopkins missed the extra point.

"You can see we're starting to turn the corner when you're not quite as ecstatic as you normally would be after a win," Gruden said. "I think there are a lot of things we can correct, clean up obviously, but I'm impressed."

Washington took the game's opening kickoff and drove 75 yards for a touchdown. Cousins was 4 of 4 for 57 yards on the drive, including a 23-yard screen pass to Thompson and 11-yard strike to wide receiver Josh Doctson for the score.

The 49ers have been outscored 37-13 in the first quarter this season.

Late in the first quarter, the Redskins took over on their 36 and 10 plays later were in the end zone. On third-and-1 from the 3, Cousins faked the handoff to Samaje Perine then passed to the rookie running back in the flat and Perine scored his first NFL touchdown.

With Washington leading 17-0 and under two minutes remaining, Beathard completed passes of 20, 30 and 12 yards to get San Francisco across midfield for the first time and down to the Redskins 13. Seven snaps later -- on the last play of the half -- Hyde scored from 1 yard out.

NOTES: Redskins head coach Jay Gruden said DL Jonathan Allen (foot sprain) and CB Bashaud Breeland (knee/MCL) will undergo MRIs Monday. ... Redskins starters CB Josh Norman (rib), RB Rob Kelley (ankle) and S DeShazor Everett (hamstring) were out. ... 49ers LB Reuben Foster (ankle) missed his fifth game. LB Brock Coyle started in place of the recently released NaVorro Bowman. S Eric Reid was active for the first time since Week 2. ... 49ers rookie QB C.J. Beathard is the grandson of former Redskins GM Bobby Beathard. ... Washington has scored an opening-drive touchdown in three straight games for the first time since Weeks 13-15 in 2004. ... The Redskins snapped a four-game losing streak against the 49ers.