SANTA CLARA – With the exception of one painful game, the 49ers have been one of the NFL’s best third-down offenses this season while converting at a clip higher than 54 percent.

That one exception, coming during the key Week 18 clash with the Seattle Seahawks, was a big difference in the game and ultimately cost the 49ers home-field advantage throughout the playoffs.

Not only did their inability to convert third downs prevent the offense from doing much damage, but it also opened the door for the Seahawks to own the time of possession battle and ultimately wear down San Francisco’s defense.

That’s something coach Kyle Shanahan says has to change if the 49ers are to have any chance of taking another step in their quest for a sixth Lombardi trophy — something he said he saw signs of during a 64-yard drive late in the second half against Seattle on Jan. 3.

“It was just more of when another team holds the ball for a while, similar to what we did in the first game, on how on point you have to be,” Shanahan said Tuesday. “Whether that’s doing better on first and second down so you avoid as many third downs as we did. If you don’t do that, you’ve got to do good on third down.”

The 49ers converted only 2 of 9 third downs against the Seahawks during their regular-season finale loss at Levi’s Stadium, the second coming on their longest drive of the game.

Nearly half of their third-down opportunities were long down-and-distance situations. On the nine third downs, quarterback Brock Purdy was intercepted three times, sacked once and threw short of the first-down marker twice, including a 1-yard completion on 3rd-and-2.

Seattle also held the ball for more than 38 minutes, putting San Francisco in a hurried mode nearly every time it got possession in the second half.

Considering all that, Shanahan said, the outcome was predictable.

“When a team holds the ball that long, if you’re not doing the same … ‘I’m moving the chains well,’ or I’m playing at a high level on third down,’ … That’s usually how it’s going to be.”

Right guard Dominick Puni said the issues against the Seahawks in the Week 18 loss were a combination of Seattle’s defense playing well and the 49ers’ offense not.

“They were doing some really good things on defense, and on offense we weren’t playing our best game,” Puni said. “Starts with me and anybody else that had a (missed assignment) in the game or just wasn’t clean. No offense wants to be in 3rd-and-8-plus. It just makes your life harder.”

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