Gardner sustained a minor bump on his head, but did not come out of the game and said he was fine afterward.
"It's unfortunate it hit me where it did, but it is what it is," Gardner said. "I got a hard head, so it's all good."
The play happened in the fourth inning of Toronto's 2-0 victory over New York at Yankee Stadium. The Blue Jays completed a three-game sweep of the Yankees to move within 1.5 games of the American League East division lead.
After Bautista connected against Yankees right-hander Masahiro Tanaka and launched his 26th homer of the season off the facade of the second deck in left field to give the Blue Jays a 2-0 lead, a fan sitting in the stands fired the ball back on the field and struck Gardner directly in the back of his head.
The incident was captured and posted to the Internet via Vine.
Home fans throwing opposing home run balls back onto the field is a tradition, but rarely if ever do they hit players. Gardner said he does not care about the tradition.
Gardner did not hear any apology from the fan.
"I think they were probably saying I suck, I think. I'm not sure," Gardner said, jokingly. "I try to block them out most of the time. The home run [Jose] hit was so far -- I don't know how far the ball got thrown back in, but it wasn't like it was coming in from the second row. So whoever hit me I probably couldn't have heard them if they tried to say anything anyway. It is what it is."
Later in the game, Yankees first baseman Mark Teixeira nearly injured his left arm while trying to make a catch in foul territory in the ninth inning. Teixeira lunged into the stands, but was unable to make the play. Before he could get up, a fan looking to grab the foul ball got tangled up with Teixeira, who became very angry. The fan quickly backed away and appeared to apologize.
"We need to tell the fans, 'You can insult, but you cannot assault,'" Teixeira said. "We know you're upset. We lost three in a row. We're sorry. But just keep it to insults, not assaults."