Week 1: at New Orleans Saints

The Niners began their Super Bowl defense on the road and raced to a 24–9 lead despite injury to Steve Young (accidentally kicked in the back of his neck) that necessitated play by Elvis Grbac for part of the first half. Two second-half Saints scores only closed the final to 24–22 Niners.

Week 4: at Detroit Lions

The Niners suffered their first defeat of the season in a 27–24 loss at the 0–3 Lions. The game lead tied or changed four times in the second half and a last-second Niners field goal attempt failed.

Week 11: vs. Dallas Cowboys

In one of the biggest upsets of the year, the injury-depleted 49ers thrashed the Cowboys 38–20. Coming into this game, the Cowboys were the NFL's best team, with an 8–1 record. The 49ers, on the other hand, were sitting at 5–4 coming off disappointing losses to New Orleans and the expansion Panthers by a combined score of 24–14. Steve Young was out with injury and Elvis Grbac was the 49ers' starting quarterback, but he had consistently struggled, completing 55 passes for 570 yards but with four INTs. As a result, the Cowboys were 14-point favorites coming in.

On just the second play of the game, Grbac split two defenders and hit Jerry Rice for an 81-yard touchdown, putting the 49ers up 7–0. On the ensuing possession, Michael Irvin fumbled the ball and it was picked up by Merton Hanks for a 38-yard touchdown, putting the 49ers up by two touchdowns just 1 minute and 24 seconds into the game. On the Cowboys' ensuing drive, they again turned it over (Troy Aikman interception) that resulted in a 49ers field goal. The 49ers led 17–0 just 4 minutes and 58 seconds into the game. By halftime, the 49ers had an astonishing 31–7 lead and held on for the win, upsetting the red-hot Dallas Cowboys. The Cowboys turned the ball over four times in the game, while the 49ers had no turnovers.

NFC Divisional Playoffs: vs. (3) Green Bay Packers

The 49ers, who were almost 10-point favorites in the game, were upset by the visiting Green Bay Packers. Green Bay set the tone early with a Craig Newsome 31-yard fumble return for a touchdown, and never looked back. Even though Steve Young had more pass attempts, completions and passing yards than his counterpart 1995 League MVP Brett Favre, he failed to throw for a touchdown and finished with 2 interceptions. The 49ers had 4 turnovers in the game. This was the final game for 49ers wide receiver John Taylor.