Fernandez joins the Whitecaps on a one-year loan with a transfer option, while Mezquida was acquired via transfer, both from Uruguayan side Boston River.
Both deals are pending receipt of their International Transfer Certificates, Canadian work permits and visas.
"Sebastian and Nicolas are exciting young attacking players with a lot of potential," Whitecaps head coach Carl Robinson said in a release. "Both players like to play with the ball on the ground and are not afraid to attack defenders one-on-one with pace."
Fernandez, 24, joins the Whitecaps after capturing the 2013 Peruvian Primera Division championship with Universitario de Deportes while on loan from Liga MX side Chiapas FC.
The five-foot-seven 165-pound Fernandez scored five times in 26 appearances for Universitario, with two of those goals coming in the playoffs.
Mezquida, 22, comes to Vancouver having last been a member of Uruguayan Primera Division side Centro Atletico Fenix.
The five-foot-six, 150-pound Mezquida joined Fenix in March 2012, and played parts of two seasons with the club. During that time, he was loaned to Uruguay's second tier side Rampla Juniors Futbal Club, where he scored seven goals in 24 appearances.