| Offensive Starters | | | | | |
| QB | Alex Smith | 27 | 6 | 16 | 273 for 445, 3,144 yards, 17 td, 5 int, & 52 rushes for 179 yards and 2 td | |
| RB | Frank Gore* | 28 | 6 | 15 | 282 rushes for 1,211 yards, 8 td, & 17 catches for 114 yards and 0 td | |
| FB | Bruce Miller | 24 | Rook | 8 | 4 rushes for 8 yards, 0 td, & 11 catches for 83 yards and 1 td | |
| WR | Michael Crabtree | 24 | 2 | 14 | 72 catches for 874 yards, 4 td, & 1 rush for 6 yards and 0 td | |
| WR | Josh Morgan | 26 | 3 | 5 | 15 catches for 220 yards, 1 td | |
| TE | Vernon Davis | 27 | 5 | 16 | 67 catches for 792 yards, 6 td, & 2 rushes for -5 yards and 0 td | |
| LT | Joe Staley* | 27 | 4 | 16 | | |
| LG | Mike Iupati | 24 | 1 | 16 | | |
| C | Jonathan Goodwin | 33 | 9 | 16 | | |
| RG | Adam Snyder | 29 | 6 | 13 | | |
| RT | Anthony Davis | 22 | 1 | 16 | | |
| Defensive Starters | | | | | |
| LDE | Ray McDonald | 27 | 4 | 15 | 5.5 sacks, 0 interceptions, 1 fumble recovered | |
| NT | Isaac Sopoaga | 30 | 6 | 15 | 0.0 sacks, 0 interceptions, 1 fumble recovered | |
| RDE | Justin Smith*+ | 32 | 10 | 16 | 7.5 sacks, 0 interceptions, 1 fumble recovered | |
| LOLB | Ahmad Brooks | 27 | 5 | 16 | 7.0 sacks, 0 interceptions, 0 fumbles recovered | |
| LILB | NaVorro Bowman+ | 23 | 1 | 16 | 2.0 sacks, 0 interceptions, 3 fumbles recovered | |
| RILB | Patrick Willis*+ | 26 | 4 | 13 | 2.0 sacks, 1 interception, 2 fumbles recovered | |
| ROLB | Parys Haralson | 27 | 5 | 16 | 2.0 sacks, 0 interceptions, 0 fumbles recovered | |
| LCB | Carlos Rogers* | 30 | 6 | 16 | 0.0 sacks, 6 interceptions, 0 fumbles recovered | |
| RCB | Tarell Brown | 26 | 4 | 16 | 0.0 sacks, 4 interceptions, 0 fumbles recovered | |
| SS | Donte Whitner | 26 | 5 | 15 | 0.0 sacks, 2 interceptions, 3 fumbles recovered | |
| FS | Dashon Goldson* | 27 | 4 | 14 | 0.0 sacks, 6 interceptions, 1 fumble recovered | |
Roster