Case Play 2014-3: What of an Extra Ball on the Field?

An extra ball flew onto Cleveland's playing field during play, producing confusion that ultimately resulted in an out at third base. With none out and two on (R1, R3), Indians batter Yan Gomes hit a double off Reds pitcher Johnny Cueto to deep right field and off the outfield wall, where it was fielded by right fielder Jay Bruce, who threw to cut-off man second baseman Kris Negron to shortstop Zack Cozart, who threw to third baseman Ramon Santiago as Indians R1 David Murphy, who had rounded third base, attempted to dive back into the bag as the tag was applied, resulting in the inning's first out as called by 3B Umpire Gerry Davis.

Replays indicate that during play and while the live ball was being thrown back towards the infield, Reds pitcher Jumbo Diaz, warming in the right field bullpen, completely airmailed a practice toss over the outfield fence and onto the playing field, where the bullpen ball coincidentally rolled toward F4 Negron, who was busy catching F9 Bruce's throw. After being tagged out at third, R1 Murphy pointed toward the second, unauthorized baseball as the argument was picked up, to no avail, by Terry Francona.

Question: Is this the proper call and application of rules? If not, what should have transpired and what rule(s) or interpretation (e.g., MLBUM) supports this? If any runners should be placed, do so (if applicable).

This Case Play is of the Group variety and expires no earlier than the final out of the final regularly scheduled game Friday, August 8. Participants may receive up to two UEFL points for discussion and solution.

Wrap: Cincinnati Reds vs. Cleveland Indians, 8/5/14
Video: Reds 'pen airmails a pitch, throwing a second baseball on the playing field, distracting Murphy