As a sophomore in 2006, Savery again earned third-team all-America status despite making only 11 pitching starts due to injury. At the plate, Savery hit .335 and was one of Rice's most dangerous postseason hitters, earning MVP honors in that year's conference tournament and making the all-regional team. He also hit a three-run home run in the decisive third game of the NCAA super regional against Oklahoma, helping the Owls to the 2006 College World Series. At the College World Series, Savery went 3-for-3 in Rice's opening-game win against Georgia but was just 1-for-9 after that.