Balotelli opened the scoring for Brescia but Ciro Immobile struck twice after Andrea Cistana's red card to turn it around for the visitors.
During the game, a warning was read out over the stadium's public address system after chants appeared to be aimed at Balotelli.
The Italy striker used social media after the match to hit out at Lazio supporters.
Sconfitta che fa male ma ci rifaremo siamo sulla strada giusta. Laziali presenti oggi allora stadio VERGOGNATEVI! #saynotoracism✊🏾🤬 Is a lost that hurt but we will come back stronger and we are on the right way! Lazio fans that were today at the stadium SHAME ON YOU! #saynotoracism ✊🏾
"[It] is a loss that hurt but we will come back stronger and we are on the right way!" He posted on Instagram with a clip of his goal.
"Lazio fans that were today at the stadium SHAME ON YOU! #saynotoracism."
It is not the first time former Milan and Manchester City striker Balotelli has been the target of abuse since he signed for hometown club Brescia at the start of this season.
In the same month, there was a controversy involving Brescia president Massimo Cellino, who said Balotelli is "black and is working on lightening up, but he is facing troubles".
The word 'nero' in Italian means 'black' but can also be used for 'gloomy'. Brescia defended Cellino's comments as "a paradoxical joke, clearly misunderstood, released in an attempt to defuse excessive media exposure and with intent to protect the player himself".