Alejandre tied with Makinano in the final outing with 6.5 points.
But Alejandre, who subdued Richard Natividad in the final round using the Sicilian opening in 54 moves, registered higher tie-break points to ran away with P3, 000.
Makinano, who defeated Voltaire Sevillano in the final round, finished second and pocketed P2, 000.
Francis Abugho beat Gamaliel Regis for third place after posting 6.0 points followed by Allan Salientes, who trounced Kim Steven Yap to wound up fourth place.
Natividad and Sevillano landed fifth and sixth, respectively.
Other players in the top ten were Carlo Saludsud, who defeated Rey Flores, Gerion Tolentino, who blanked Erwin Ababat, Yap and Regis.