| Offensive Starters | | | | | |
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| QB | John Brodie | 31 | 9 | 13 | 232 for 427, 2,810 yards, 16 td, 22 int, & 5 rushes for 18 yards and 3 td | San Francisco 49ers / 1st / 3rd pick / 1957 |
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| HB | John David Crow | 31 | 8 | 14 | 121 rushes for 477 yards, 1 td, & 30 catches for 341 yards and 3 td | Chicago Cardinals / 1st / 2nd pick / 1958 |
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| FB | Ken Willard* | 23 | 1 | 14 | 191 rushes for 763 yards, 5 td, & 42 catches for 351 yards and 2 td | San Francisco 49ers / 1st / 2nd pick / 1965 |
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| FL | Bernie Casey | 27 | 5 | 13 | 50 catches for 669 yards, 1 td, & 1 rush for 23 yards and 0 td | San Francisco 49ers / 1st / 9th pick / 1961, New York Titans / 9th / 69th pick / 1961 |
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| SE | Dave Parks* | 25 | 2 | 13 | 66 catches for 974 yards, 5 td, & 1 rush for -1 yards and 0 td | San Francisco 49ers / 1st / 1st pick / 1964, San Diego Chargers / 4th / 32nd pick / 1964 |
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| TE | Monty Stickles | 28 | 6 | 14 | 27 catches for 315 yards, 2 td | San Francisco 49ers / 1st / 11th pick / 1960 |
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| LT | Len Rohde | 28 | 6 | 14 | 1 fumble recovered | San Francisco 49ers / 5th / 59th pick / 1960 |
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| LG | John Thomas*+ | 31 | 8 | 14 | 1 fumble recovered | San Francisco 49ers / 23rd / 272nd pick / 1957 |
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| C | Bruce Bosley* | 33 | 10 | 14 | 2 fumbles recovered | San Francisco 49ers / 2nd / 15th pick / 1956 |
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| RG | Howard Mudd* | 24 | 2 | 14 | | San Francisco 49ers / 9th / 113th pick / 1964 |
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| RT | Walt Rock | 25 | 3 | 14 | | Kansas City Chiefs / 2nd / 16th pick / 1963, San Francisco 49ers / 2nd / 21st pick / 1963 |
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| Defensive Starters | | | | | |
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| LDE | Jim Norton | 24 | 1 | 11 | | San Francisco 49ers / 3rd / 30th pick / 1965 |
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| LDT | Charlie Krueger | 29 | 7 | 14 | 0 interceptions, 1 fumble recovered | San Francisco 49ers / 1st / 9th pick / 1958 |
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| RDT | Roland Lakes | 27 | 5 | 14 | | San Francisco 49ers / 2nd / 24th pick / 1961, Boston Patriots / 9th / 66th pick / 1961 |
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| RDE | Clark Miller | 28 | 4 | 14 | | San Francisco 49ers / 5th / 58th pick / 1961, Oakland Raiders / 14th / 108th pick / 1961 |
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| LLB | Dave Wilcox* | 24 | 2 | 14 | | San Francisco 49ers / 3rd / 29th pick / 1964, Houston Oilers / 6th / 46th pick / 1964 |
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| MLB | Ed Beard | 27 | 1 | 12 | | Oakland Raiders / 20th / 159th pick / 1964, San Francisco 49ers / 14th / 183rd pick / 1964 |
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| RLB | Matt Hazeltine | 33 | 11 | 12 | 1 interception, 1 fumble recovered | San Francisco 49ers / 4th / 45th pick / 1955 |
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| LCB | Jimmy Johnson | 28 | 5 | 14 | 4 interceptions, 2 fumbles recovered | San Francisco 49ers / 1st / 6th pick / 1961, San Diego Chargers / 4th / 31st pick / 1961 |
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| RCB | Kermit Alexander | 25 | 3 | 14 | 4 interceptions, 4 fumbles recovered | Denver Broncos / 1st / 5th pick / 1963, San Francisco 49ers / 1st / 8th pick / 1963 |
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| LS | Elbert Kimbrough | 28 | 5 | 14 | 3 interceptions, 2 fumbles recovered | Los Angeles Rams / 2nd / 18th pick / 1961, Oakland Raiders / 4th / 28th pick / 1961 |
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| RS | George Donnelly | 24 | 1 | 7 | 2 interceptions, 1 fumble recovered | San Francisco 49ers / 1st / 13th pick / 1965, Denver Broncos / 4th / 25th pick / 1965 |
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| Special Teams Starters | | | | | |
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| K | Tommy Davis | 32 | 7 | | 16 of 31 field goals & 38 of 39 extra points | San Francisco 49ers / 11th / 128th pick / 1957 |
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| P | Tommy Davis | 32 | 7 | | 63 punts for a 41.4 average, 0 blocked | San Francisco 49ers / 11th / 128th pick / 1957 |
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| PR | Kermit Alexander | 25 | 3 | 14 | 30 punt returns for a 6.6 average and 1 td | Denver Broncos / 1st / 5th pick / 1963, San Francisco 49ers / 1st / 8th pick / 1963 |
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| KR | Kermit Alexander | 25 | 3 | 14 | 37 kick returns for a 26.6 average and 0 td | Denver Broncos / 1st / 5th pick / 1963, San Francisco 49ers / 1st / 8th pick / 1963 |
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