You'll need to deal with those glowing Psi-Emitters first, there are 3 of them spread around the rooftop arena (they look like red lantern devices and you can't miss them). This setup actually makes a lot of sense, because destroying them gradually weakens his defensive capabilities. Keep moving between cover spots while you take them out, and watch for those Monolithian troops that'll spawn in to protect the emitters. Once you've handled the structural emitters, look for that distinct glowing device on Faust's hip - that's his personal emitter and the real source of his invincibility. Taking this out finally makes him vulnerable to damage.

Maybe interesting: bringing a shotgun makes the emitter destruction much quicker, and staying relatively close to Faust helps avoid those nasty psi-grab attacks he loves to use. The spawned enemies are actually more dangerous than Faust himself at first, so don't ignore them completely while focusing on the emitters.

A quick bit of knowledge that might help - this strategy works the same way regardless of which story path you chose earlier, whether you went with "Happiness for Everyone" or "Once More Unto the Breach" (these choices affect other things but not this fight mechanics).