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SANTA CLARA — What had been a respectable showing for the 49ers’ pass defense — or at least an improvement over its last outing — all went up in smoke once Carson Palmer had the ball in his hands with 2:24 to go in overtime.

Some miscommunication in the 49ers’ secondary opened the door just enough for the Arizona Cardinals quarterback to find Larry Fitzgerald open for a 19-yard touchdown with 32 seconds left in overtime, handing San Francisco a gut-wrenching 18-15 loss Sunday.

Prior to the touchdown, Palmer completed 5 of 7 passes for 58 yards on the decisive drive, taking advantage of the 49ers’ zone defense on the first two plays then finding a soft spot in coverage on the game-winning throw.

Up until overtime, the 49ers had held Palmer to a reasonable 240 passing yards, and sacked him six times.

That would have represented a vast improvement over the 292 yards they allowed to Jared Goff and the Los Angeles Rams 10 days prior. Goff was not sacked and threw for three touchdowns Sept. 21 at Levi’s Stadium. The 49ers have now allowed 961 passing yards this season, ninth most in the NFL.

Palmer began the drive with a pair of 11-yard completions to Andre Ellington, quickly moving the ball to the Arizona 47 with 1:54 to go in the extra session.

“When you play zone with a four-man rush, you drop and they checked it down to the back right away,” 49ers coach Kyle Shanahan said Monday. “We want those to be five-yard gains. We’ve got to break to the ball a little bit faster, make better tackles in that situation.”

Just before the touchdown, the only one of the game, NaVorro Bowman picked up a shoe that had come off Ellington’s foot. He flung it out of the way, returned, then got the call from the 49ers’ sideline as to what defense to run for the next down.

The sequence of events might have been just enough to throw off the 49ers for the game-deciding play.

“Things are going fast, you’re trying to get the communication in for the calls, you get it to NaVorro, he relays it to the D-linemen, the secondary,” Shanahan said. “(Arizona) got up there, they got set fast, and there was just a little hesitation in our secondary.

“We ended up getting to the right spots, but we were a foot behind, and when you do that versus a good quarterback and especially (Fitzgerald) going down the seam, they made us pay.”

Bowman was emphatic after the game that officials should have blown the whistle to make sure the shoe was not in anybody’s way.

Shanahan said, “We ended up being on our assignments. We were a little off our landmarks.”

Fitzgerald ran past nickel back K’Wuan Williams and had inside position on Rashard Robinson, giving Palmer a sizable target for the throw. The 49ers had three safeties in the game with four linebackers.

“We were off on a little bit of everything,” Shanahan said about the play. “So, there was a bigger hole in the zone than there normally is, and Carson threw a very good ball to a very big body, and they got us.”

Part of the Cardinals’ winning drive was a defensive pass interference call against Jimmie Ward, giving Arizona first and 10 at the San Francisco 27-yard line. The 49ers were penalized 13 times for 113 yards on Sunday, and now have a league-worst 39 penalties against this season.

“It’s going to be tough to overcome some things when you have those types of penalties,” Shanahan said.