Bernier was one of many second basemen to appear for the Rockies in 2008. With the departure of starter Kazuo Matsui prior to the season, the Rockies struggled to find a replacement. Bernier competed for the role with teammates Jayson Nix, Jeff Baker, and Omar Quintanilla before the position was awarded to former starting shortstop Clint Barmes.
On June 20, 2008, Bernier was optioned back to Triple-A Colorado Springs to open a roster spot for returning shortstop Troy Tulowitzki. On June 26, he was removed from the 40-man roster and became a free agent at the end of the season.
In December 2008, Bernier signed a minor-league contract with the New York Yankees, and attended spring training as a non-roster invitee. Although compiling a solid spring performance in an attempt to land a roster spot as starter Robinson Canó's backup, Bernier was reassigned to the Triple A Scranton/Wilkes-Barre Yankees at the beginning of the 2009 season.