| 12 Sep 99 | r01        | Jacksonville JaguarsJacksonville | 41 - 3 | San Francisco 49ersSan Francisco |
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| 19 Sep 99 | r02        | San Francisco 49ersSan Francisco | 28 - 21 | New Orleans SaintsNew Orleans S |
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| 28 Sep 99 | r03        | Arizona CardinalsArizona Cardi | 24 - 10 | San Francisco 49ersSan Francisco |
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| 03 Oct 99 | r04        | San Francisco 49ersSan Francisco | 24 - 22 | Tennessee TitansTennessee Tit |
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| 10 Oct 99 | r05        | Los Angeles RamsLos Angeles R | 42 - 20 | San Francisco 49ersSan Francisco |
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| 17 Oct 99 | r06        | San Francisco 49ersSan Francisco | 31 - 29 | Carolina PanthersCarolina Pant |
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| 24 Oct 99 | r07        | Minnesota VikingsMinnesota Vik | 40 - 16 | San Francisco 49ersSan Francisco |
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| 07 Nov 99 | r09        | San Francisco 49ersSan Francisco | 27 - 6 | Pittsburgh SteelersPittsburgh St |
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| 14 Nov 99 | r10        | New Orleans SaintsNew Orleans S | 24 - 6 | San Francisco 49ersSan Francisco |
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| 21 Nov 99 | r11        | San Francisco 49ersSan Francisco | 23 - 7 | Los Angeles RamsLos Angeles R |
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| 30 Nov 99 | r12        | San Francisco 49ersSan Francisco | 20 - 3 | Green Bay PackersGreen Bay Pac |
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| 05 Dec 99 | r13        | Cincinnati BengalsCincinnati Be | 44 - 30 | San Francisco 49ersSan Francisco |
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| 12 Dec 99 | r14        | San Francisco 49ersSan Francisco | 26 - 7 | Atlanta FalconsAtlanta Falco |
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| 18 Dec 99 | r15        | Carolina PanthersCarolina Pant | 41 - 24 | San Francisco 49ersSan Francisco |
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| 27 Dec 99 | r16        | San Francisco 49ersSan Francisco | 26 - 20 | Washington CommandersWashington Co |
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| 04 Jan 00 | r17        | Atlanta FalconsAtlanta Falco | 34 - 29 | San Francisco 49ersSan Francisco |