He's not untouchable - he just regenerates - so you have to beat him a bunch of times.

You can use 'Drain Life' (dark-side power) to replenish your own health from the captive jedi, and simultaneously deny him that source of health. Makes the end-fight much easier for dark-side players.

Just finished the game for the first time 2 hours ago...I used force lightning.
Had to reload a few times for that final fight (my character probably wasn't optimal), but on the whole I have to say the game's too easy, most of the fights feel like mindless hackn'n slash.

As using Drain Life on the captured Jedi also replenishes your Force points, it can also be done as Light Side character, if you've picked that power (I did as the last one, as I only intended to use it in Malak fights).

With Jedi's pragmatism, "I did what I had to do" etc. thing, it could even make sense In Character/from RP point of view (They were dead anyway, killing them for good you're doing them a favor. And stripping Malak of his healing sources, too).

Fair-enough - but choosing 'drain life' as a level-up power would be more of a dark-side choice IMO - it's not like your character knows about the end-game.

You can also use droid countering powers (Stun/Disable/Destroy droid) to destroy the life support systems keeping the captured Jedi alive. You won't recover force nor health, but you'll still keep Malak from replenishing his own.

True, it was ultimately a gameplay choice that I made with defeating Malak in mind.

However, using Kyle Katarn's words - when he was already a Jedi Master (in Jedi Knight: Jedi Academy), he said something along the line of, it's not what powers do you use, but why/to what goal. By that logic, using "Dark" power of Drain Life in order to defeat Malak might be considered a-okay by Jedi standards (especially since I actually first tried to turn him back to Light side, and only fought him when that failed - oh, and actually apologised for first leading him down the "dark path" too, afterwards).

Also I'm not sure if picking powers in the first place is anything but Gameplay and Story segregation - in the movies, we don't see, say, Luke advancing in levels, and picking Force Speed, or Force Persuade power, etc.

Even if it isn't though, it could be explained without much of a stretch as some remnants/resurfacing of Revan's power/memories. Or him not being as perfect a Jedi as there are. Etc.

Throw Lightsaber / Advanced Throw Lightsaber is another ability that works to "free" the Jedi from the machines (and prevent Malak leeching from them).