Black was ejected by first base umpire Brian Knight after Knight ruled that Cameron Maybin was out at first base on a headfirst slide on a ground ball to Reds second baseman Brandon Phillips.
Television replays indicated that Maybin beat Phillips' throw.
This was the third ejection this season for Black.
"That was probably the most upset I've been on the baseball field in a while," Black said. "It's a situation where it kind of changed the game a little bit. First and third with one out, we've been playing well, so you want those calls to go your way. He [Knight] missed it, it happens."
With the Reds leading 1-0, Yonder Alonso doubled with one out. Maybin tapped a ball to Phillips, who came in fast on the play and scooped up the ball before throwing it to first baseman Joey Votto.
Maybin, who stole 40 bases last season and is regarded as the fastest player on the team, protested for a moment, before Black intervened. Black argued his case to Knight and was then ejected.
Alonso advanced to third base on the play but was left stranded after Mat Latos struck out Everth Cabrera to end the inning.
The Padres eventually tied the game on pinch-hitter Logan Forsythe's home run to left field to start the bottom of the eighth.
The Padres won the game when Cabrera singled with the bases loaded in the bottom of the ninth.
"I think it fired everybody up," Maybin said of Black's ejection. "Just the play in itself and the skipper having my back on that, it's huge. I think our whole team, our whole dugout just felt that, vibed off of that, and responded really well."