Fajardo and Sergio Villahermosa ended with identical 5.5 points, but Fajardo got the title via the tiebreak where he had 28.5 Buchholz against 22.5 of Villahermosa.
Fajardo opened his bid with two straight wins but lost his third game to his officemate Alex Verano.
Fajardo bounced back in the next two rounds and engaged into another difficulty ending with a draw with Ludendorf Caña in the sixth round.
In the seventh and final round, Fajardo pulled the wins over erstwhile leader Benjamin Rodriguez paving his way to victory.
The third to 10th placers were Roden Roble, Philip Romero, Benjamin Rodriguez, Ludendorf Caña, Ernesto Eata, Arturo Cañares and Julius Colinares.
In related development, Francisco Abugho added excitement in tournament after posting seven wins and a draw in an 8-board simultaneous exhibition.