Gwynn, who was inducted into the Baseball Hall of Fame in 2007, was the head coach of Mountain West member San Diego State University from 2002 until his death.
The league's baseball coaches made the recommendation in August, and it was recently approved by the conference's governing council.
Gwynn was a two-time All-American outfielder for the Aztecs after batting .423 in 1980 and .416 in 1981. He was subsequently drafted by the Padres and the then-San Diego Clippers after also starring as a basketball point guard.
With the Padres, the 15-time All-Star won eight National League batting titles and became a fan favorite. His son, Tony Jr., also played at SDSU and is now a member of the Philadelphia Phillies.
The naming of the award will take effect next season. The uniforms for players on Mountain West teams will also display a TG logo on their uniforms next year, according to the Mountain West.