The 27-year-old's extension also has club options for the 2016 ($7.5m) and 2017 ($10m) season that would bring his new contract to $27.5 million over five years.
The one-year, $500K deal Luebke signed earlier in the offseason now turns into a nice signing bonus with the new deal.
Appearing in just four games for the Padres in 2010, Luebke made the San Diego bullpen at the start of 2011 and pitched well. In 29 appearances and 39 IP, the lefty had a 3.23 ERA and held batters to a .183/.267/.244 line.
Moved to the starting rotation at the end of June, Luebke held his own, throwing 100 innings over 17 starts and maintaining a 3.31 ERA.
Overall, in 46 appearances in last season Luebke racked up a 3.29 ERA in 139 2/3 innings, striking out more than a batter per frame.