The play occurred in the top of the fifth inning, coming right after Manoah had hit another Athletics player, Josh Harrison, up and in.
Harrison threw his bat in frustration and vocalized his displeasure as he walked to first base.
The Athletics dugout was visibly upset by the back-to-back wayward pitches but did not spill out onto the field.
After being hit, Marte initially stayed in the game.
Matt Olson made Manoah and the Blue Jays pay shortly after, hitting a two-run double that put the Athletics up 4-2 at the time.
Oakland's dugout erupted as Marte scored, after which he left and did not return.
The team has not yet provided an update on his condition. Skye Bolt replaced him in centre field.
Errant pitches that hit players have not been uncommon for Manoah this season. In 14 starts, he has made contact with batters nine times.