Clayton Beathard, 22, was at a bar when there was an argument over a woman.
It spilled outside, and he was stabbed to death along with another man during the fight.
A third person was injured, and the suspect got away.
C.J. Beathard will not be at Saturday's 49ers game and has gone home to Nashville.
Clayton was the starting quarterback for Long Island University and just finished his junior season.
The 49ers released a statement saying:
"The 49ers family was shocked and deeply saddened to learn of the tragedy involving C.J. Beathard's younger brother, Clayton. We extend our heartfelt sympathies to C.J. and the entire Beathard family as they cope with the unthinkable loss of a loved one. C.J. has traveled home to join his family knowing he has the support of our entire organization as they grieve the passing of Clayton."
Niner CEO, Jed York, sent his condolences on Twitter.
Stay with ABC7 News for the latest developments.