DG: Delay of Game, FS: False Start, HLD: Holding, OFF: Offsides, IC: Illegal Contact, PI: Pass Interference, RP: Roughing the Passer, PF: Personal Foul, UR: Unnecessary Roughness, UC: Unsportsmanlike Conduct
| Penalties | Penalty Breakdown | |||||||||||||
| Player | Pos | Team | Num | Yds | FS | HLD | OFF | IC | PI | RP | PF | UR | UC | Other |
| Olivea, Shane | OT | SD | 9 | 66 | 6 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
| Phillips, Shaun | DE | SD | 7 | 44 | 0 | 1 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 3 |
| Florence, Drayton | DB | SD | 6 | 51 | 0 | 1 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 2 |
| Dielman, Kris | OG | SD | 5 | 50 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 |
| McNeill, Marcus | OT | SD | 5 | 25 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Rivers, Philip | QB | SD | 4 | 32 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 |
| Jackson, Vincent | WR | SD | 4 | 24 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 |
| Williams, Jamal | DT | SD | 3 | 45 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 |
| Merriman, Shawne | LB | SD | 3 | 15 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Cromartie, Antonio | DB | SD | 2 | 33 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 |
| Kiel, Terrence | DB | SD | 2 | 30 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
| Jammer, Quentin | DB | SD | 2 | 29 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| Turner, Michael | RB | SD | 2 | 20 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 |
| Wilhelm, Matt | LB | SD | 2 | 20 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Cesaire, Jacques | DT | SD | 2 | 15 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Gates, Antonio | TE | SD | 2 | 15 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Gregory, Steve | DB | SD | 2 | 15 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 |
| Edwards, Donnie | LB | SD | 2 | 13 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| Hardwick, Nick | C | SD | 2 | 10 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Harris, Marques | LB | SD | 2 | 10 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Hart, Clinton | DB | SD | 2 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 |
| Tomlinson, LaDainian | RB | SD | 2 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 |
| Jue, Bhawoh | DB | SD | 1 | 22 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| McCree, Marlon | DB | SD | 1 | 18 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| Castillo, Luis | DT | SD | 1 | 15 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| Cooper, Stephen | LB | SD | 1 | 15 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Goff, Mike | OG | SD | 1 | 15 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Olshansky, Igor | DT | SD | 1 | 15 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Robinson, Derreck | DE | SD | 1 | 15 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Godfrey, Randall | LB | SD | 1 | 14 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Camarillo, Greg | WR | SD | 1 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Lott, Andre | DB | SD | 1 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| Neal, Lorenzo | RB | SD | 1 | 10 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Withrow, Cory | C | SD | 1 | 9 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Manumaleuna, Brandon | TE | SD | 1 | 5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| McCardell, Keenan | WR | SD | 1 | 5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Osgood, Kassim | WR | SD | 1 | 5 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
