Brooks' agent, Greg Williams, said his client would appeal the penalty -- the standard fine for such hits to the head and neck area.
Brooks was penalized for a personal foul, which negated a sack and fumble and enabled the Saints to maintain possession for a game-tying field goal by Garrett Hartley in the fourth quarter. The Saints won 23-20 as Hartley made another field goal as time expired.
Brees described the hit as a clothesline tackle, with the initial contact taking place at the chest and going across his neck and chin as he went to the ground.
Brooks was fuming after the game, incredulous that he was penalized for the hit.
"I didn't hit him with my hand or my helmet," Brooks told reporters, according to the San Francisco Chronicle. "I basically bear-hugged him. That's just how football is played. I think this s--- is bulls----. Football, the way they call stuff these days, it's watered down. It ain't real no more."
Brees told reporters Tuesday he doesn't think the hit was malicious, or even intentional, but that he believes it was a penalty.
"I don't think what Ahmad Brooks did was intentional at all," Brees said. "I think he's a heck of a football player and a clean football player. A hard-nosed, clean football player.
"But you look at the result of that & and again in real time & you can slow it down all you want and watch it and say, 'Look where the [arm is].' But I can tell you how I felt when I got hit. It felt like I got my head ripped off. And I get up and I've got a mouth full of blood. So there was no doubt in my mind that, 'Hey, it's gonna be a penalty.'"
49ers coach Jim Harbaugh said Monday that he thought Brooks' hit was legal.
"When we grade a player, if he has a penalty, we give him a minus," Harbaugh said, according to the team's website. "We did not assign a minus on that play. Thought he made a great play, just didn't get the result."
On Tuesday, NFL vice president of officiating Dean Blandino said the officials in Sunday's game got the call right.
"You can't make forcible contact to the head or the neck area, even if the contact starts below the neck and rises up," Blandino said in an appearance on NFL Network. "If there's force to that contact, it's a foul. Watch the initial contact, maybe around the shoulder, but it rides up into the neck area and brings the quarterback down with force. That's why the flag was thrown for unnecessary roughness."
ESPN NFL Insider Adam Schefter, ESPN.com 49ers reporter Bill Williamson and Saints reporter Mike Triplett and information from The Associated Press contributed to this report.