As the ball went over his head, he made a desperate attempt to come up with the punt, but it went bouncing toward the end zone. San Francisco recovered the ball at the Chicago two-yard line.
Against most teams it would have led touchdown, but the 49ers were unable to capitalize on the mistake.
The Bears defense deserves credit for keeping San Francisco out of the end zone when they had a chance to tie the game. On first down Hunter Hillenmeyer stopped RB Kevin Barlow for no gain.
Cody Pickett used a bootleg to get outside the pocket on second down. He looked to have a clear path to the end zone, but Brian Urlacher stopped him for a one-yard gain and Adewale Ogunleye jumped in to help finish the play.
Everything fell apart for the 49ers on third down. To have 12-men in the huddle when you would have snapped the ball from the one-yard line is inexcusable. The miscue got the crowd going and San Francisco collapsed under the pressure. A delay of game penalty pushed them back another five yards.
"I could tell right away after warm-ups there was a lot of energy in the crowd," said safety Mike Brown. "They caused them a lot of trouble. They forced a couple false starts, a delay of game penalty so they were a huge factor in today's game."
First and goal from the 2 quickly turned into third and goal from the 11. Throughout the game, San Francisco went with the run on third and long, but had to let Pickett try to make a play.
Brandon Lloyd appeared to be open on a slant route but failed to come up with the low throw from Pickett, who completed just one pass on the day.
The 49ers had to settle for a field goal to cut the lead to 14-9, but the damage could have been much worse considering the circumstances.
Chicago has ranked atop the NFL in red zone defense the entire season and that strength helped beat San Francisco.
Three trips inside the 20 resulted in nine points. In 22 red zone opportunities on the season, opponents have four touchdowns, 11 field goals, two missed field goals, three turnovers and two possessions end because of time expiring.
With first and goal, the competition has only reached the end zone twice out of 11 chances.
Opponents have an 18 percent touchdown conversion rate when they get inside the 20. Heading into today's game, the next closet unit was the Dallas Cowboys at 35.3 percent.
"You don't score until you cross that goal line, that's our philosophy," Brown said. "We're going to make everyone earn everything they get. We have a really good scheme down there on the goal line. We're real aggressive down there and we have guys that make plays."