The two sides were separated by just one point prior to kick off at the Estadio Heraclio Tapia Leon in Huanuco, but the hosts advanced inside the top half of the table.
An own goal from Cajamarca's Rafael Farfan was the difference, the defender getting the final touch into his own net in the 50th minute.
Further disadvantaging Jose Hernandez's visitors was the 74th-minute dismissal of defender Manuel Corrales, who was previously cautioned on the stroke of half-time.
The result was Leon de Huanuco's third win in five, while Cajamarca are winless in their past five matches.
Leon de Huanuco can build on their promising form in the coming weeks, with fixtures against mid-table sides Real Garcilaso and Universidad San Martin before a date with the high-flying Juan Aurich.
Cajamarca sit 12th of 16 teams in the Peruvian top flight, but go up against two sides below them next - Sporting Cristal and cellar-dwellers Los Caimanes - in a prime period for them to boost their flailing fortunes.
