It might work for awhile as a temporary repair, but RTV silicone isn't the correct way to seal it up, and the leak will still persist since the leak will allow water in from anywhere around the window, usually.
The correct way to fix this is to use new 3M butyl rubber tape, which is what seals the window from the factory. The 1/4 inch size is what you need, it's about $12-15 for a roll at the parts store, or body shop, though usually you'll have to order it in, and most places only stock the 3/8 inch size, which is too thick and will have the side windows sticking out from the body. You will also want to use the 3M adhesion primer (~$25 for a 125ml size) as well, since it lets the butyl seal adhere to the window and the body better, making for a longer lasting seal so you won't be doing this again in a few years.
Trouble is, the adhesion primer can be hard to come by. I was able to order in the tape and the primer at CarQuest for an extremely reasonable price over what a body shop that carried 3M prodicts wanted.
Once you have the materials, you'll need to remove the interior panel, so you can get to the nuts holding the window in. Remove the nuts, and slowly, gently push out the window, hopefully with someone else outside the vehicle to catch it once it pops loose. You'll want to use 3M adhesive remover to clean up the residue from the old seal on the window and the vehicle, making note of how the old seal was located around the window. Once it's clean and dry, apply the primer, let it dry, then put the rubber seal on the window as close as you can match the original path, take it to the vehicle, line up the mounting studs, and do your best to stick it on in one motion. Once it's stuck, it's tuck, and if you have it crooked or one corner with a stud not fully inserted, it will be a struggle to free it up.
You get enough butyl tape in a roll to do both windows, so if you have the time, you could do both rear windows one after the other, to prevent the other side leaking, which it will eventually do if one side had it happen.
I would suggest doing this ASAP, I didn't find out until too late that the window was the cause of the leak, and it eventually leaked long enough that it soaked the under carpet insulation, and pooled in the rear compartments, rusting the rear floor to the point I had to cut and weld in new metal behind the left fenderwell.
I would suggest pulling the rear carpet and floor panels out, in case they absorbed water at some point, and letting them air dry on a sunny day, or even indoors for a few days to allow them to fully dry. It will make it easier to remove the rear interior panels anyway.
Some places will tell you to just use urethane adhesive that comes in a tube. It IS simpler, you just put the tube in a caulk gun, stick it on either surface, and it's sealed. Forever. The problem is, the window will never come off ever again, so repairing a craked window or any body work on the rear panel will be a heck of a job. If you take it to a glass shop and have them do it, they will likely use urethane adhesive, and charge you ~$100 a side to do it.
even though I checked it with the hose after I put it back on and it was sealed
