The San Diego Chargers were in the 1994 Super Bowl (Super Bowl XXIX). They lost to the San Francisco 49ers 49-29.
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That was Super Bowl XXXVII played January 26, 2003 at Qualcomm Stadium. The Buccaneers defeated the Raiders, 48-21.
The last time the 49ers were in the Super Bowl was in Super Bowl XXIX in 1995. They played against the San Diego Chargers.
Final score: San Francisco - 49, San Diego - 26
Super bowl xxix was the only time they made it and lost to the San Francisco 49ers.