After all of the trapped Jedi are destroyed, all you have to do is take off Malak's last health bar and you win. Unlike some of the more annoying Dark Jedi you've run into, Malak won't spam death fields at you; he doesn't appear to have any way to heal himself at all, as a matter of fact.
The same general tactics from the beginning of the fight will hold true for the duration: increase the number of attacks you get per round, without sacrificing attack bonus, while maintaining a constant energy shield and keeping your vitality above the halfway mark. If you drop to near-death, Malak will start chaining together Force lightning attacks, which will penetrate most energy shields easily, and kill you in a couple of rounds.
If you note that you're almost dead and/or almost out of Force points, do the smart thing and start running away. If you switch off of Malak with the B button and get a distance away from him, your Force points should start regenerating, since the game won't think that you're in a battle anymore. If you do this long enough, you should gain enough Force points for a few emergency cures, though you may have to run for an even longer period of time afterward for another complete Force point recharge before taking on Malak again. It's tedious, but it works; just be sure you keep moving, or Malak will likely get in position for a Force jump.
If you find yourself having an extremely difficult time connecting with a lightsaber, you can go the unconventional route and attempt to take down Malak with grenades. He'll usually stay right on top of you, but he will occasionally pause to use a Force power like Force breach. If you can catch him when he's standing still and chuck a thermal detonator at him, he'll be knocked off his feet, allowing you to throw another detonator in the next round, which should also knock him down. If you have enough detonators, you should be able to repeat the process until he dies. It'll take around 15 detonators, though, which will probably be more than you've come across in the entire game, unless you've been buying them, so you will still probably have to engage in at least some saber combat.
That first step's a doozy, especially when a dozen mines are waiting for Malak's foot.
The absolute cheesiest way to off Malak, though, is via the handy use of the demolitions skill and a few deadly mines. Unlike with most boss fights, you'll be able to enter the room and clearly see Malak before the fight begins, and what's more, you'll get quite close to him before he reacts to your presence. If you stop a couple meters short of the end of the metal walkway that leads into the room, then lay down mines, you can easily lure him across after you dispense with all of the trapped Jedi. A mix of five deadly frag mines and five deadly plasma mines is enough to almost completely kill Malak, even when he has a full health bar; just make sure you've cleared out all of the trapped Jedi first, because you obviously only get one shot at this. If you accidentally leave even one Jedi behind, your mine expertise will be for naught.
Malak will fall eventually. And that, as they say, is that. The game does, if you're curious, have different endings for Light side and Dark side characters (how could it not?), but we won't spoil those for you. If you have a savegame from just before the fight with Bastila, you can reload that and make a different choice to see the other ending, but the game lends itself well to a complete replay.