This is near the beginning of Priority: Thessia. It's the encounter that's just after Outpost Tykis (where you find the M-560 Hydra, aka the weapon that can one-shot a Banshee) and is between you and the entrance to the Temple of Athame.
Is it possible to kill both Harvesters at this point? Should I even try? I noticed that they flew away after the other fighter ship after a while, but I'm wondering if I would get a bonus to War Assets or something if I was able to save the other pilot and/or if I was only able to kill say, one, make a later battle somewhat easier. Or is the event with the pilot completely scripted and unalterable?