Then he didn't stand tall in the game, either.
While both social and the national media clearly cared more about the former, 49ers coaches and fans had to be much more concerned about the latter.
Kaepernick did take time after the game to explain his stance on the anthem in an interview with NFL Media.
"I am not going to stand up to show pride in a flag for a country that oppresses black people and people of color," he said. "To me, this is bigger than football and it would be selfish on my part to look the other way. There are bodies in the street and people getting paid leave and getting away with murder."
The 49ers and NFL issued subsequent statements, both noting that while they encourage standing for the anthem, there are no rules against it.
Kaepernick is not expected to be disciplined.
But shortly after his sitdown strike, he threw far too few strikes on the field to accomplish his goal, which had been to overtake Blaine Gabbert in the team's quarterback competition.
Gabbert made his third consecutive start and was decent, which was similar to his first two outings. After a three-and-out on the 49ers' first series, Gabbert completed both pass attempts for 14 yards during a five-play, 53-yard touchdown drive.
New 49ers coach Chip Kelly seemed more critical of Gabbert's play.
"We've had some missed passes to start a game," he said. "It's something, obviously, that we need to clean up because you don't want to start the game with a three-and-out."
In other words, the door was open for Kaepernick to shine. But it didn't happen.
He got three series, during which the 49ers recorded one first down. It came on his best pass of the game, a 12-yard throw to DeAndrew White.
But he went just 1-for-5 on his other throws, completing a pass for two yards and rushing four times for 18 yards.
Coincidentally, his production (14 yards passing, 18 yards rushing) was almost identical to that of Gabbert (14 yards passing, 15 yards rushing). It's just that it took Gabbert only three throws and two runs to get his numbers.
And then there's that touchdown drive, the biggest thing in Gabbert's favor.
Kaepernick felt the stadium, after his NFL Media interview, believing the competition wasn't over.
"I think next game we have to be more productive, put points on the board. Ultimately, that's what you want to do as an offense and as a quarterback," he said of Thursday's preseason finale against the San Diego Chargers (10 p.m. ET). "So, I think that will be a big thing for next week."
At his day-after press conference Saturday, Kelly insisted the competition is not over.
"We haven't had any discussions in terms of starters right now," Kelly said.
-- Here are the statements made by San Francisco and the NFL in the wake of Kaepernick failing to stand for the national anthem:
"The national anthem is and always will be a special part of the pre-game ceremony," the 49ers said. "It is an opportunity to honor our country and reflect on the great liberties we are afforded as its citizens. In respecting such American principles as freedom of religion and freedom of expression, we recognize the right of an individual to choose and participate, or not, in our celebration of the national anthem."
"Players are encouraged but not required to stand during the playing of the national anthem," the NFL said.
Kaepernick noted that the sitdown was planned and that only he knew it was going to happen.
"This is not something that I am going to run by anybody," he told NFL Media. "I am not looking for approval. I have to stand up for people that are oppressed.
"If they take football away, my endorsement from me, I know that I stood up for what is right."
Asked about the incident and its possible impact on relationships inside the locker room Saturday, Kelly said Kaepernick had done the same thing at the Denver game last week and it didn't seem to bother anyone.
"We haven't gotten any feedback from any of our players," he claimed. "We'll talk about it as a team. We'll talk about it (Monday)."
-- The 49ers debuted what now appears to be their starting offensive line in the game, inserting Joshua Garnett at left guard and Anthony Davis at right guard. They replaced Zane Beadles and Andrew Tiller.
Garnett and Davis began training camp on the third unit, Garnett because he had missed all the summer drills while finishing up at Stanford, and Davis because he had been in retirement.
The 49ers lost left guard Alex Boone in free agency during the offseason, and replaced him with Beadles, their biggest free-agent signing. Beadles started at left guard on Day 1 of camp.
Kelly said after the game that no decision has been made on the starting offensive line, labeling it "an evaluation."
-- The 49ers appear to have suffered three significant injuries during the game.
Carlos Hyde suffered a concussion and has entered the NFL's concussion protocol, meaning he's unlikely to practice this week.
Starting nose tackle Quinton Dial left the game with a knee injury. He was sent for an MRI on Saturday.
The 49ers made no statement about the severity of the injury, but it was being reported as a strained ligament. If so, Dial would be unlikely to be ready for the regular-season opener against the Los Angeles Rams.
Starting wideout and kick returner Bruce Ellington also got an MRI on Saturday after suffering a hamstring injury in the game. As with Dial, the 49ers offered no details at Kelly's media availability Saturday.
Backup nose tackle Mike Purcell (arm) and free safety Eric Reid (thumb) were pulled from the game with what at the time were considered minor injuries. In fact, Reid was able eventually to return to the game.
-- The 49ers' roster was cut down to 79, four over the limit, on Saturday by trading cornerback Kenneth Acker to Kansas City, placing wideout Eric Rogers on season-ending injured reserve, and releasing nine players - including wideout Jerome Simpson.
The 49ers received a seventh-round pick in return for Acker, a sixth-round pick in 2014 who started 13 games and intercepted three passes last season.
Also waived were: running back Kendall Gaskins, wide receiver DiAndre Campbell, offensive linemen Blake Muir and Ian Silberman, defensive lineman Darren Lake, linebacker Wynton McManis, cornerback Cleveland Wallace and place-kicker John Lunsford.
The 49ers must be down to the 75-man limit by noon Tuesday.