| Passing | G | Comp | Att | Pct | Yds | Y/A | Y/G | TD | Int | Long | Sack | Yds/L | Fum | FumL |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Alex Smith | 5 | 95 | 155 | 61.3 | 1035 | 6.7 | 207.0 | 9 | 7 | 40 | 13 | 76 | 2 | 1 |
| Shaun Hill | 6 | 87 | 155 | 56.1 | 943 | 6.1 | 157.2 | 5 | 2 | 61 | 18 | 107 | 3 | 1 |
| Micheal Spurlock | 4 | 0 | 1 | 0.0 | 0 | 0.0 | 0.0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| Rushing | G | Rush | Yds | Y/G | Avg | Long | TD | Fum | FumL |
|---|---|---|---|---|---|---|---|---|---|
| Frank Gore | 8 | 112 | 610 | 76.3 | 5.5 | 80 | 6 | 2 | 0 |
| Glen Coffee | 9 | 75 | 198 | 22.0 | 2.6 | 17 | 1 | 0 | 0 |
| Shaun Hill | 6 | 8 | 70 | 11.7 | 8.8 | 22 | 0 | 3 | 1 |
| Alex Smith | 5 | 8 | 41 | 8.2 | 5.1 | 11 | 0 | 2 | 1 |
| Moran Norris | 10 | 10 | 32 | 3.2 | 3.2 | 15 | 0 | 0 | 0 |
| Josh Morgan | 10 | 3 | 25 | 2.5 | 8.3 | 11 | 0 | 0 | 0 |
| Delanie Walker | 10 | 1 | 16 | 1.6 | 16.0 | 16 | 0 | 0 | 0 |
| Micheal Spurlock | 4 | 1 | 3 | 0.8 | 3.0 | 3 | 0 | 1 | 0 |
| Michael Robinson | 10 | 2 | 3 | 0.3 | 1.5 | 4 | 0 | 0 | 0 |
| Isaac Bruce | 9 | 1 | -8 | -0.9 | -8.0 | -8 | 0 | 0 | 0 |
| Receiving | G | Rec | Yds | Y/G | Avg | Long | YAC | 1stD | TD | Fum | FumL |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Vernon Davis | 10 | 51 | 601 | 60.1 | 0.0 | 40 | 189 | 26 | 8 | 0 | 0 |
| Josh Morgan | 10 | 24 | 305 | 30.5 | 101.7 | 61 | 153 | 12 | 1 | 0 | 0 |
| Michael Crabtree | 5 | 22 | 292 | 58.4 | 0.0 | 38 | 68 | 14 | 1 | 1 | 1 |
| Isaac Bruce | 9 | 21 | 264 | 29.3 | 264.0 | 50 | 62 | 13 | 0 | 0 | 0 |
| Frank Gore | 8 | 29 | 220 | 27.5 | 2.0 | 35 | 216 | 8 | 2 | 2 | 0 |
| Delanie Walker | 10 | 5 | 81 | 8.1 | 81.0 | 39 | 52 | 3 | 0 | 0 | 0 |
| Glen Coffee | 9 | 10 | 69 | 7.7 | 0.9 | 12 | 96 | 2 | 0 | 0 | 0 |
| Jason Hill | 5 | 6 | 63 | 12.6 | 0.0 | 30 | 37 | 4 | 2 | 0 | 0 |
| Arnaz Battle | 10 | 5 | 40 | 4.0 | 0.0 | 12 | 21 | 3 | 0 | 0 | 0 |
| Moran Norris | 10 | 4 | 23 | 2.3 | 2.3 | 11 | 19 | 1 | 0 | 0 | 0 |
| Michael Robinson | 10 | 5 | 20 | 2.0 | 10.0 | 8 | 20 | 1 | 0 | 0 | 0 |
| Field Goals | PAT | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Kicking | G | 0-19 | 20-29 | 30-39 | 40-49 | 50+ | FGM | FGA | Pct | Long | XPM | XPA |
| Joe Nedney | 10 | 0-0 | 2-2 | 5-6 | 3-5 | 1-1 | 11 | 14 | 76.1 | 50 | 25 | 25 |
| Kickoff Returns | Punt Returns | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Returns | G | KR | Yds | FC | Avg | Long | TD | PR | Yds | FC | Avg | Long | TD |
| Michael Robinson | 10 | 17 | 402 | 1 | 23.7 | 40 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 |
| Allen Rossum | 3 | 7 | 152 | 0 | 21.7 | 40 | 0 | 12 | 84 | 1 | 7.0 | 14 | 0 |
| Josh Morgan | 10 | 2 | 101 | 0 | 50.5 | 76 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 |
| Delanie Walker | 10 | 4 | 81 | 0 | 20.3 | 25 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 |
| Arnaz Battle | 10 | 3 | 68 | 0 | 22.7 | 26 | 0 | 5 | 5 | 5 | 1.0 | 3 | 0 |
| Glen Coffee | 9 | 1 | 13 | 0 | 13.0 | 13 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 |
| Kentwan Balmer | 10 | 2 | 7 | 0 | 3.5 | 4 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 |
| Nate Clements | 7 | 0 | 0 | 0 | 0.0 | 0 | 0 | 4 | 38 | 1 | 9.5 | 12 | 0 |
| Brandon Jones | 5 | 0 | 0 | 0 | 0.0 | 0 | 0 | 6 | 7 | 0 | 1.2 | 4 | 0 |
| Reggie Smith | 4 | 0 | 0 | 0 | 0.0 | 0 | 0 | 3 | 7 | 0 | 2.3 | 9 | 0 |
| Punting | G | Punt | Yds | Avg | In20 | In10 | TB | Long |
|---|---|---|---|---|---|---|---|---|
| Andy Lee | 10 | 61 | 2924 | 47.9 | 19 | 4 | 4 | 64 |
| Tackles | Interceptions | Misc. | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Defense | G | Solo | Ast | Total | Sack | YdsL | Int | Yds | IntTD | PD | Sfty |
| Patrick Willis | 10 | 70 | 26 | 96 | 2.5 | 15 | 2 | 27 | 1 | 6 | 0 |
| Dashon Goldson | 10 | 55 | 9 | 64 | 1.0 | 0 | 2 | 2 | 0 | 3 | 0 |
| Michael Lewis | 9 | 43 | 11 | 54 | 0.0 | 0 | 1 | 0 | 0 | 2 | 0 |
| Manny Lawson | 10 | 34 | 12 | 46 | 3.5 | 25 | 0 | 0 | 0 | 0 | 0 |
| Takeo Spikes | 9 | 28 | 14 | 42 | 1.0 | 10 | 0 | 0 | 0 | 0 | 0 |
| Shawntae Spencer | 10 | 34 | 3 | 37 | 0.0 | 0 | 1 | 2 | 0 | 7 | 0 |
| Justin Smith | 10 | 24 | 11 | 35 | 1.0 | 18 | 0 | 0 | 0 | 0 | 0 |
| Nate Clements | 7 | 30 | 5 | 35 | 0.0 | 0 | 1 | 8 | 0 | 7 | 0 |
| Mark Roman | 10 | 28 | 4 | 32 | 1.0 | 9 | 1 | 27 | 0 | 2 | 0 |
| Aubrayo Franklin | 10 | 18 | 8 | 26 | 2.0 | 14 | 1 | 10 | 0 | 1 | 0 |
| Parys Haralson | 10 | 18 | 4 | 23 | 2.0 | 18 | 0 | 0 | 0 | 1 | 0 |
| Isaac Sopoaga | 10 | 12 | 7 | 19 | 1.0 | 8 | 0 | 0 | 0 | 1 | 0 |
| Tarell Brown | 10 | 15 | 3 | 19 | 0.0 | 0 | 1 | 51 | 0 | 4 | 0 |
| Marcus Hudson | 8 | 13 | 1 | 17 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Dre' Bly | 10 | 13 | 2 | 15 | 0.0 | 0 | 1 | 31 | 0 | 8 | 0 |
| Matt Wilhelm | 5 | 7 | 5 | 13 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Scott McKillop | 10 | 10 | 1 | 13 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Delanie Walker | 10 | 10 | 0 | 13 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Kentwan Balmer | 10 | 5 | 6 | 11 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Michael Robinson | 10 | 8 | 0 | 10 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Arnaz Battle | 10 | 6 | 0 | 6 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Marques Harris | 4 | 3 | 1 | 6 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Glen Coffee | 9 | 4 | 0 | 6 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Ray McDonald | 10 | 5 | 1 | 6 | 3.0 | 19 | 0 | 0 | 0 | 0 | 0 |
| Ahmad Brooks | 8 | 6 | 0 | 6 | 1.0 | 9 | 0 | 0 | 0 | 1 | 0 |
| Brian Jennings | 10 | 3 | 0 | 6 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Curtis Taylor | 6 | 3 | 0 | 4 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Demetric Evans | 8 | 2 | 2 | 4 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Josh Morgan | 10 | 4 | 0 | 4 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Allen Rossum | 3 | 1 | 0 | 2 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Michael Crabtree | 5 | 2 | 0 | 2 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Micheal Spurlock | 4 | 1 | 0 | 2 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Jason Hill | 5 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Adam Snyder | 10 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Reggie Smith | 4 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Chilo Rachal | 10 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Moran Norris | 10 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Isaac Bruce | 9 | 1 | 0 | 1 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 |