He can launch a Lightning Bolt from his sword if you attempt a frontal attack. He will also use it with his Templar Vision to launch an attack against your hiding spot.
The Lightning Blast from before can be used as well. If you linger too long in one place, there is a good chance he will call down a blast. Watch around Arno's feet for a yellowish aura.
Immediately move forward to the next pillar in the line. Germain will be trying to hunt you down and kill both Arno and Elise. As he paces in the center of the room, make your way around to the left. With some patience, he will eventually have a long time with his back to Arno. Sneak up behind him for a hit against him.
When Arno does connect, he will be blown back by the released electricity. Once he recovers, immediately run for cover. You just need to get close to Germain twice more to trigger the next cutscene.