The league and the Jaguars had raised copyright, trademark and other objections to certain features on the newspaper's Internet site, including electronic post cards of players and contests.
Officials of the Jacksonville, Fla., newspaper, which is owned by Morris Communications Corp. of Augusta, had said the Internet site is an extension of the printed newspaper.
On Monday, a disclaimer added to the newspaper's Jaguars Web page noted that it is not the official Jaguars Web page.
"We will make sure there is no confusion between our site and the Jaguars' site," Times-Union Publisher Carl Cannon said. "We want people to know that it is our site."
The newspaper, National Football League officials and the Jaguars, represented by vice president of marketing Dan Connell, resolved their differences at a meeting.
"We had a good exchange of ideas and a better understanding and appreciation of each other's position," said Mr. Connell, who spoke on behalf of the Jaguars and the NFL.