Replays showed catcher Yan Gomes' throw from his knees took Lonnie Chisenhall into the sliding Inciarte and the tumbling third baseman applied the tag before the baserunner reached the bag.
The replay review overturned the call on the field in 46 seconds.
Francona had contemplated challenging a play at first base in the top of the inning on a grounder by Jason Kipnis, but elected not to after receiving word from the Indians' dugout.
Chris Gabel is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.