You can cut holes in metal with a jigsaw, yes. I've done it a few times, just make sure you're using a metal blade! You get blades meant for different things; don't mix them up, disaster can occur. (Well the worst that happens is you ruin a blade).
You will have to make an initial incision with either a drill or a dremel to begin with, then it should be smooth sailing for the jigsaw.
If you're looking to make a fan hole, I really don't recommend using a jigsaw for that; it's going to be all kinds of difficult. You could use either a dremel with a reinforced cutting disk or a hole saw to cut fan holes in your case.
4.5" hole saw is what you need for 120mm fans, and the screw holes to mount the fans should be 4mm/ 0.15".