NEW ORLEANS — A strong argument could be made that the much-maligned New Orleans Saints defense played well enough to win Sunday at the Mercedes-Benz Superdome.

But that would be throwing quarterback Drew Brees under the proverbial bus, and no teammate in his right mind would ever do that, despite the fact he threw two game-changing pick-sixes in their 31-21 loss to the NFC West-leading San Francisco 49ers.

“You can always say ‘what if?’ but it is what it is,’’ Saints free safety Malcolm Jenkins said. “Yeah, they scored twice on interceptions, but, as a defense, we could have held them to field goals instead of allowing touchdowns like we did.

“We dug ourselves a big hole today, but they’re a good football team.’’

Believe it or not, a victory Sunday against the 49ers (8-2-1) would have moved the Saints (5-6) into the sixth NFC playoff spot after Seattle (6-5), Tampa Bay (6-5) and Minnesota (6-5) lost earlier in the day.

But it wasn’t to be.

“That’s fabulous,’’ Jenkins said sarcastically when informed by a reporter of his team’s squandered opportunity. “Pouring a little salt in the wound, aren’t you? Thank you.

“No, that’s OK. We got to find a way to come up with some wins.’’

The Saints had their chances against the 49ers and second-year quarterback Colin Kaepernick, who started his second consecutive game for injured starter Alex Smith.

And for the second straight game, Kaepernick acquitted himself well, completing 16 of 25 passes for 231 yards and accounting for two touchdowns. He scored from 7 yards out on a read-option in the first quarter and threw a 6-yard scoring pass to running back Frank Gore in the third quarter.

Then, he directed a clinching 16-play, 85-yard drive that lasted 9 minutes, 28 seconds and ended with David Akers’ 27-yard field goal for a 31-21 lead with 7:50 left in the game.

Overall, the Saints yielded just 375 yards against the 49ers, snapping a string of 12 consecutive games during which New Orleans’ opposition had eclipsed the 400-yard mark dating to the 2011 playoffs. Despite their solid performance, the Saints remain the NFL’s 32nd-ranked defense, yielding an average of 454.8 yards through 11 games.

“I guess you could take some positives from this game,’’ Saints weakside linebacker Jonathan Vilma said. “But I’ll be honest in that I don’t take positives away from a loss. We aren’t one of those teams that goes for moral victories.’’

“We didn’t play complementary ball today,’’ Saints linebacker Jonathan Casillas said. “If our offense hadn’t given up two pick-sixes, it probably would have been a different game. But there are things we could have done on our side of the ball, and we didn’t do them.

“We should have stopped them a few more times than we did.’’

Throughout the week, 49ers coach Jim Harbaugh worked hard to keep his starting quarterback under wraps, ultimately forcing the Saints to prepare for both Smith and Kaepernick.

Smith was active for Sunday’s game after being cleared by doctors Saturday for concussion-like symptoms, but he never saw the field.

“They had the same game plan for Kaepernick as they would have had for Smith,’’ Vilma said. “Kaepernick did extend some plays for them, but so does Smith. But I thought Kaepernick did a good job of keeping his cool and managing their offense.’’

The Saints now must quickly turn their attention to Thursday night’s primetime rematch against the NFC West-leading Atlanta Falcons (10-1) at the Georgia Dome. The Saints handed the Falcons their first defeat of the season after starting 8-0, winning 31-27 in Game 9 at the Superdome.

“So now the margin for error is much more slim for us,’’ Vilma said. “There is no time to mourn over this loss. We got Atlanta on Thursday at their place, and they’re a good team, too.’’