I recently dealt with a similar problem -- I installed a water accessory and was faced with a 3/8" compression male outlet and nothing needing to be connected to it. A cap was easy to find at the plumbing supply but it didn't seal well. Wrapping the male thread with teflon tape plus pipe dope slowed the leak to a very slow drip, but the fact is the threads on a compression joint just aren't intended to form a seal.
In this case I got away with sealing it by placing a thick o-ring in the bottom of the cap. It sealed the cap to the male fitting nicely.
I was concerned the o-ring might wrinkle or buckle in some way during assembly, allowing the leak to continue. Had that happened I also considered carefully placing a brass or acetyl/delrin ferrule (without any tubing) into the male fitting, then place the o-ring around that, and finally install the cap. Maybe the ferrule would seal between the fitting and the cap, but if it didn't, it could provide some structure to help keep the o-ring in place.