To upgrade your augments you'll require praxis points, for which you'll either come across by chance, through a seller, or by earning the experience on your own. Once you're unable to locate or purchase praxis any further, the only way to rank up from there on out is to keep leveling.
In other words, it is possible to upgrade every ability you have. It's just going to take a lot of time to do so. I had unlocked about 90% of the powers myself (maybe somewhere around 10 of them were left to pay off). At the very end of the game there is still at least one or more praxis kits left to find, just as there is plenty of enemies afoot to give you experience.