The Super Bowl champion Chiefs allowed less than 17,000 fans inside the normally rocking 75,000-seat Arrowhead Stadium and required the spectators to wear masks and stay socially distant during the game.
The first seven rows of the stadium were left empty to create a "moat" to prevent any transmission of the virus between fans and players.
The league has left it up to the 32 teams and local officials to decide if it is safe to allow spectators into their stadiums with coronavirus outbreaks flaring in much of the country, where it has claimed more than 190,000 lives.
As the season starts, six teams have said they will have fans in the stands including the Dallas Cowboys. Others like the Chicago Bears and Las Vegas Raiders have shuttered stadiums for the entire season.
Most are taking a week-by-week approach, leaving the door open for a possible partial return of spectators if or when conditions permit.
Since quarterback Patrick Mahomes and his team raised the Lombardi trophy in early February, the issue of racial injustice and police brutality has exploded in the wake of several high profile deaths of Black people by police.
It did not take long for the protests to make their mark on the league's 101st season as the Houston Texans left the field during the playing of the "Lift Every Voice and Sing," often called the Black national anthem, and the "Star-Spangled Banner."
The Texans said they didn't want to choose between celebrating one song and "throwing shade" on the other so decided to return to their locker room.
The Chiefs remained on the field for both songs with the players locking arms during them. Only Chiefs linebacker Alex Okafor took a knee during the "Star-Spangled Banner," a gesture popularized by San Francisco's Colin Kaepernick in 2016, which created controversy.
In July, the NFL said it would play both anthems before all Week One games. Earlier on Thursday the Miami Dolphins released a video saying they would stay inside their locker room during the playing of the songs, calling the NFL's move "an empty gesture."
Thursday's game was the first since the Chiefs won the championship 221 days ago as there was no pre-season.