A couple of hours earlier, David Ortiz, slated to make his first start of the season at first base, was also scratched for the same reason and replaced by Sean Casey.
Though the Red Sox are still mathematically alive in the race for the American League East title, they are placing more of a priority on making sure their team is healthy for the postseason.
The Red Sox would have to sweep the Yankees this weekend and the Rays would have to lose all three of their games in Detroit in order for Boston to win the AL East.
Otherwise, the Red Sox will go into the postseason as the AL Wild Card entry and face the Los Angeles Angels of Anaheim in a Division Series matchup that would start in Anaheim next week.
Matsuzaka is likely to pitch Saturday's 3:55 p.m. ET game against the Yankees. Josh Beckett had originally been penciled in to pitch that game, but all along, the Red Sox were vague as to whether the ace right-hander would get the start.
Beckett is all but certain to pitch Game 1 of the Division Series for the Red Sox next week, whether it is played on Wednesday or Thursday.
Pauley had made five outings for the Red Sox this season, just one of which was a start. The righty spent most of the season at Triple-A Pawtucket.
Ian Browne is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.