With that large a hole I'd recommend using a patch rather then attempting to fill in the "cavity" with a sealant.

You will need to find some of that aluminum skin material and that should not be too hard to find. You'll need about a one foot square. Take a small plate/saucer, turning upside down and out like a round patch ... you want it round, not square (no points to come loose and catch on something).  For an adhesive/sealant you'll want either a urethane seam sealer or a two part epoxy (both available at an automotive body shop supply store).

Start out by cleaning the surface so there nothing to interfere with adhesion (I'd use a 70% isopropyl alcohol).  Scuff the area (lightly sand), clean it again, and try to pull up the jagged edges of puncher to almost level. Where there's still an opening cover that with a small bit of masking tape so the sealant will not ooze down through it.  Apply the sealant to be used (use a Bondo spreader) on both the repair surface and on the the bottom side of the patch.  Press into place right where you want it, wipe the excess sealant off around the edge (again, alcohol) and place something like a gal milk jug (full of water) over the patch to hold it firmly in place.  When dry, you good to go, except if you need/want to paint the area, but if the aluminum patch material is the same color as the p'up roof I'd let go as is.