Dean Anna of the Yankees was originally ruled safe on a double in the eighth inning of Saturday's 7-4 win. A television replay showed his right foot briefly came off the base as he stood up with shortstop Xander Bogaerts tagging him.
Red Sox manager John Farrell challenged the call. Moments later, Anna was ruled safe.
MLB said the conclusive angle showing Anna was out wasn't immediately available inside the replay booth in New York.
No one scored after the play.
''I felt like I was on the whole time,'' Anna said.
Said Farrell: ''We probably had five angles that confirmed his foot was off the base.''
''It certainly raises questions on if they are getting the same feed we are, the consistency of the system,'' he said. ''So, it makes you scratch your head a little bit on why he was called safe.''