As it turned out, it was Rams quarterback Case Keenum who squatted on the final play of the 28-0 game, completing the Los Angeles surrender.
Kelly, as he had promised in the preseason, treated Kaepernick like any ol' backup quarterback even after another of his pregame "statements."
The former Super Bowl starter was inserted into the game well after the outcome was decided.
"We've said from Day 1: We recognize their right to do it; it's their constitutional right," Kelly said of Kaepernick and others choosing not to stand at attention during the national anthem. "Our President said the same thing. That's part of what it's like to be an American, that you have the right to choose, and that's what he's choosing to do.
"So, I think it's a very kind of cut-and-dry situation to be honest with you."
Veteran offensive lineman Anthony Davis, another player who created a bit of a stir on the eve of the opener, got the same treatment from Kelly as Kaepernick.
He's a backup player, and will play only when the situation dictates.
Davis reportedly missed practice Saturday while he contemplated retiring for the second time in two years. He returned to the team Sunday and suited up for Monday's win.
Kelly labeled Saturday's absence a "miscommunication."
"There was just a miscommunication, but he was back on Sunday and he had a real good Sunday for us and was good (Monday)," Kelly said. "I had a long talk with Anthony on Saturday and everything has been ironed out. He's good to go."
The 49ers started Andrew Tiller at right guard and Zane Beadles at left guard in the opener. First-round pick Joshua Garnett was a surprise inactive.