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.
Midfielder Ariel Rojas pulled one back for the Mendoza team four minutes from time with a brilliant shot from outside the box that went in off the underside of the bar.
Boca are nine points ahead of second-placed Tigre whose only chance of the title is to win their three remaining matches and Boca lose theirs so they go into a play-off since goal difference is not taken into account.
Promoted Union are the only other side with an interest in the title. If they beat Independiente at home in Santa Fe on Monday they will be in the same position as Tigre, nine points behind Boca with three games to go.
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.
Juan Sebastian Veron, set to retire at the end of the championship, scored 10 minutes from time to give Estudiantes a 2-1 win at Arsenal, only their third win in 15 matches in the Apertura which they won a year ago.
"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.
Belgrano had Uruguayan midfielder Ribair Rodriguez sent off in the 66th minute and defender Juan Quiroga in the 88th along with Racing striker Gabriel Hauche after the pair kicked each other in an ill-tempered fight for the ball.
