San Francisco 49ers head coach Kyle Shanahan rued a missed opportunity after a 31-20 loss to the Kansas City Chiefs in the Super Bowl on Sunday.

The 49ers looked on track for a record-equalling sixth Super Bowl title as they carried a 20-10 lead into the final seven minutes at Hard Rock Stadium.

But Patrick Mahomes and Damien Williams led a Chiefs comeback as they scored 21 unanswered points to win their first title in 50 years.

A disappointed Shanahan, who was criticised for being too conservative during the loss, said it was a chance missed for the 49ers.

"We had opportunity to win that and we came up short. Win or lose, today doesn't change how I feel about our team," he told a news conference.

"I'm real proud of the guys, what they did all year, I'm proud of what they did today.

"Kansas City played a good game, they were better than us today and we can deal with that, but we're obviously pretty disappointed."

Jimmy Garoppolo had appeared to be guiding the 49ers to victory and the quarterback finished with 219 yards on 20 of 31 completed passes, with one TD and two interceptions.

Shanahan felt Garoppolo "played all right", instead lamenting the 49ers' inability to convert on third down in the fourth quarter.

"We didn't convert those third downs there in the fourth quarter," he said.

"When you don't convert those third downs and you don't get an explosive run, you end up giving them too many chances."