A Pittsburgh native and graduate of Carrick High School, Wehner was drafted out of Indiana University by the Pirates in the 7th round of the 1988Major League Baseball Draft and made his debut on July 17, 1991. He was in the Pirates organization, splitting his time between the majors and their minor league affiliates, through the 1996 season. In 1997 he joined the Florida Marlins as a bench player, staying there for two seasons before rejoining the Pirates in 1999.
He retired from playing in 2001 after hitting the final home run and making the final out in the history of Three Rivers Stadium. In 11 seasons in the major leagues, Wehner compiled a .249 batting average with four home runs and 54 RBI in 461 games. He has played every position except pitcher at least 3 times. He also shares the major league record of 99 consecutive errorless games at third base with Jeff Cirillo and has a World Series ring with the Florida Marlins for the 1997 season.