They're not words I use very often, but they seem to be pretty similar in meaning and could probably be used interchangeably in most cases, yes.
Definition of Partisan:
The main difference for me is that guerilla suggests a particular style of fighting too. One of harassing a more powerful army.1. A fervent, sometimes militant supporter or proponent of a party, cause, faction, person, or idea.
2. A member of an organized body of fighters who attack or harass an enemy, especially within occupied territory; a guerilla.