Attorney General Jesus Murillo Karam declared the case "resolved, " although one suspect remains at large.
Neve was himself a major collector, and owned 160 Old Master paintings, including many by Murillo.
Neve saw Murillo as an artist who could express difficult points of Catholic doctrine.
Mexico's Attorney General, Jesus Murillo Karam, said Ms Gordillo, 68, had hurt the very union she leads.
BBC: Mexico union head Gordillo charged with organised crime
"If it's an accident, if it's negligence, if it's an attack, whatever it is, " Mr Murillo Karam said.
Its chief patron and Murillo's was Justino de Neve (1625-85), canon of Seville Cathedral, and subject of the painter's superb 1665 portrait.
Jesus Murillo Karam said there was risk of structure collapse in the last two of the 39 sectors of the affected area.
Exhibited in a converted chapel flooded with light, it is the first of approximately 20 renditions Murillo made of the Virgin Mary surrounded by angelic cherubs.
Mr Murillo Karam said investigators had established that the blast had not set off a fire, but that it was not yet clear what that meant.
Authorities in Acapulco had announced the detention of several people over the weekend, but those arrests had nothing to do with the case, Murillo Karam said Wednesday.
Investigators have not yet determined whether the suspects arrested, one of whom is 16 years old and thus a minor, are part of a gang, Murillo Karam said.
Attorney General Jesus Murillo Karam said the suspects had confessed.
"It was identified that between 2008 and 2012, resources were diverted from the accounts of education workers, obviously from the union, to accounts of individual people, " Murillo Karam said.
"In Cuba, there will not be political reform, " said Marino Murillo, vice president of the island's council of ministers, responding to the pope's remarks about its Marxist political system.
By the 1900s, the cream of Spanish art was in Madrid, London or New York, while shifting tastes led contemporary critics to deride Murillo for being vacuous and overly sentimental.
Speaking to reporters, Mr Murillo said that although the last person rescued from the debris had been found at noon on Friday (1800 GMT) work would continue until all the areas had been cleared.
Because of a punning coincidence between his name and "nieve, " the Spanish for "snow, " Neve commissioned Murillo to paint two lunettes, semicircular murals depicting the founding in Rome of Santa Maria Maggiore the legend that the Virgin appeared to a Roman patrician in a dream, and told him to build the church on a hill where he'd find snow in August.
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