Estudiantes, who had won their first three matches of the Final championship, were caught at the top of the standings by title holders San Lorenzo on nine points after their 1-0 win over Quilmes.
Gigliotti headed the only goal from midfielder Fernando Gago's cross in the 43rd minute at a packed Bombonera where Boca had lost 3-2 to Belgrano behind closed doors last weekend due to a ban for crowd violence earlier in the season.
The striker, who has scored nine goals over the two-championship season, slammed the criticism record title-winning coach Carlos Bianchi has received for his team's poor run.
"They played with our pride, they spent their time talking about Boca and Bianchi, all the teams lose, Racing, River, Newell's and they just talk about Bianchi. We needed to win, this is good for our heads," he told reporters.
The crowd gave playmaker Juan Roman Riquelme a standing ovation when he came on for Gigliotti 10 minutes from time after being sidelined since November through injury.
The match also marked the debut as a substitute of winger Diego Perotti, who has returned from his loan spell at Sevilla.
Title holders San Lorenzo, winners of the Inicial championship in the first half of the season, beat relegation candidates Quilmes 1-0 with a goal from attacking midfielder Ignacio Piatti at the Nuevo Gasometro.
Newell's Old Boys also ended a poor run of 11 league matches without a victory, by crushing Atletico Rafaela 4-1 in Rosario.
Beleaguered coach Alfredo Berti, who succeeded Gerardo Martino when he left for Barcelona in July, was relieved after his position had come under question.
"It was a difficult time (for the players) and they pulled us through," Berti told reporters. "I was always calm amid the rumours because of the confidence the players give me.
"This is just the beginning," Berti said, contemplating not just the Final championship but also the South American Libertadores Cup Newell's want to win after losing the final in 1988 and 1992.