Striker Dario Cvitanich scored after nine minutes, then was brought down in the box in the 36th and central defender Rolando Schiavi converted the penalty.
"I'm more happy with the result than my goal, but we're not there yet," Cvitanich told broadcasters TV Publica at the end of the match at the Malvinas Argentinas stadium in the shadow of the Andes mountains.
Title holders Velez Sarsfield, winners of last season's Clausura, fell too far behind when their reserves were held 1-1 at home by Colon. The first team were rested for their Copa Sudamericana semi-final second leg against Ecuador's LDU Quito in mid-week.
"These are the real fans," Veron said of the travelling Estudiantes supporters after his angry verbal exchange with a group of hooligans who threw flares onto the pitch and caused Monday's home game against Banfield to be abandoned.
Racing Club, coached by Veron's former Argentina team-mate Diego Simeone, lost their unbeaten record in a 3-2 home defeat by nine-man Belgrano on Saturday and fell 11 points adrift of Boca.
Racing conceded almost as many goals in one match as the four they had in the previous 15 with Belgrano's Cesar Pereyra on target twice.
