SANTA CLARA, Calif. — Dealing with a team as talented as the San Francisco 49ers is difficult enough in the best of circumstances.

For the New York Giants, doing it without their best offensive playmaker and best offensive lineman proved to be too much to overcome.

New York’s offense never managed to get going without Saquon Barkley and Andrew Thomas against San Francisco’s tenacious defense, with Daniel Jones spending much of the day on the run during a 30-12 loss to the 49ers on Thursday night.

“We didn’t create a rhythm, we didn’t execute, we didn’t take advantage of our opportunities,” Jones said. “Certainly it is a good defense, a good team, and so when you’re playing good teams, you can’t afford to do that. We didn’t play well enough. It was frustrating at times, but I felt like we were in the game really until the end and had chances to make plays really to the end.”

Barkley is the focal point of New York’s offense and with him on the sideline with a sprained ankle, the running game was grounded and that limited when the Giants (1-2) could do with their play-action passes.

“No excuses,” coach Brian Daboll said. “With anybody who missed the game, or who played, we have to go out there and compete and win football games.”

Jones was under heavy pressure all night from Nick Bosa and Co. and only managed to avoid being sacked more than twice by getting rid of the ball quickly and not challenging the 49ers down the field. He finished 22 for 32 for 137 yards and one interception, while managing 5 yards rushing.

The Giants had five three-and-outs and one turnover on 10 possessions, with their only touchdown coming on a drive that started at the San Francisco 37 and included a 22-yard penalty.

New York finished with 150 yards of offense, converting just 3 of 12 third-down tries. The Giants had a few opportunities to sustain drives but Jones was inaccurate on third-down passes or his receivers dropped the ball.

“We’ve got to convert a couple of those opportunities when you play a good team like that,” Jones said. “Got to be crisp and got to be clean and we didn’t do that.”

Three games into the season, the Giants have played one good half of football. They fell behind 26-0 at halftime of the opener against Dallas before losing 40-0. They trailed Arizona 20-0 at the break last week before rallying for a 31-28 win.

They found themselves in a 17-6 hole this week and never were able to climb out of it. New York’s minus-57 point differential in the first half is the worst through three games since at least 1991.

“It’s not what we’re trying to do,” Jones said. “So we’ve got to find a way to figure that out, execute better early in the game, finish in the end zone, take advantage of our opportunities. But it comes down to making plays and executing better in those situations.”

The defense wasn’t much better against San Francisco.

The 49ers posted 441 yards of offense, taking advantage of New York’s heavy blitzing to turn short passes into big gains. San Francisco was especially sharp on third down, converting 9 of 16 opportunities and getting two others on penalties.

Two of the most costly conversions came on one drive in the first half when Deebo Samuel and Christian McCaffrey turned quick passes into first downs on 3rd and 15 and 3rd and 13, respectively.

“They just outplayed us on third down,” defensive tackle Dexter Lawrence said. “We have to do better with those screens, running to the ball and getting people down.”