More than a dozen players from the San Francisco 49ers had knelt for the anthem, while members of Mr Pence’s home team, the Indianapolis Colts, linked arms in solidarity.
I stand with @POTUS Trump, I stand with our soldiers, and I will always stand for our Flag and our National Anthem.
In the NFL, some players are choosing to kneel, rather than stand, when The Star-Spangled Banner is played before games as a form of demonstration at police violence against African Americans.
The protests started when Colin Kaepernick sat down for the anthem before a game in August 2016.
He later told NFL Media he was “not going to stand up to show pride in a flag for a country that oppresses black people and people of colour.”
“To me, this is bigger than football and it would be selfish on my part to look the other way,” the San Francisco quarterback said.
“There are bodies in the street and people getting paid leave and getting away with murder.”
The wave of protest has been condemned by the US right wing and President Trump, who last month urged fans to boycott NFL games until “players stop disrespecting our flag & country”.