Banfield, who came into the game on a run of six successive defeats, were a man down for an hour after defender Marcelo Bustamente was sent off and conceded a penalty converted by striker Teofilo Gutierrez in the third minute.
Banfield equalised in the 11th minute when their goalkeeper Cristian Lucchetti had a penalty saved by his opposite number Sebastian Saja but Andres Chavez netted the rebound.
Banfield's winner, which leaves Racing with one point from three matches, came in added-time from striker Rodrigo Lopez's header at a free-kick.
"My teams go out to attack, I was hired to play like that," Basile told reporters. "We dominated but didn't create chances. We have a good team but [the opposition] always scores. I want to win, up to now I haven't found the formula."
With 11 minutes to go, Gutierrez earned a second booking and was sent off when he kicked the ball out of Lucchetti's hands as the goalkeeper was looking to throw the ball to a team-mate.
Gutierrez was booed off the Cilindro pitch by Racing's fans, who also had harsh words for Basile at the end. The 68-year-old coach retaliated angrily: "Who are you insulting? I'll fight you all."
In other matches, title holders Boca Juniors beat Newell's Old Boys 2-0 at the Bombonera to extend their unbeaten league run to 32 matches and share top place on seven points from three games with Velez Sarsfield, Tigre and All Boys.
Racing's arch-rivals Independiente are even worse off than their neighbours and languish in bottom place after three defeats, their latest 2-0 to Estudiantes in La Plata on Saturday.
