Villareal scored a 77 for 159, leaving Qroni Baterna (80) far behind with his 159 aggregate for 36 holes at the tree-lined north course of Canlubang.
He stands to join the long list of winners in his division which has been the most closely-fought so far.
Superal is also poised to become a runaway winner for the seventh straight time as he added a 65 to his spectacular 60 on Monday to submit a 125 - again a new jungolf record - going into tomorrows final round.
The 10-year-old will actually take aim at the biggest winning margin. He now stands 31 ahead of Melvin Pizarro with Don Martin Fernandez and Jovy Ong tied at 157.
Matet Salivio (girls Class A), Dottie Ardina (girls Class D), Linnel de Villa (girls Class B) and Kristina Potenciano (girls Class E) are also on their way to easy wins.
Crystal Faith Superal was also heading for a big win as Paulina Sotto, daughter of television host Vic, was 13 strokes adrift. Aaron Dimabuyo, meanwhile, inched ahead by three over Patrick Cruz in boys Class A with his 78-157 while Anelo Asistio was just up by two over Stephen Bolivar in boys Class C.