I originally thought he ****ed that line and they autotuned it in post-production. It was taped without an audience and not a live broadcast, so that wouldn't have been something too extraordinary.
However, I just compared several live performances from that era and from 2008 to 2012. On broadcast dates they might've used that backing track. The 12 12 12 concert sounds and looks lip-synced to me as well.
During live shows, I don't think it was utilized that much. They had a track for the backing vocals in the chorus ever since '95 I think (though I can't understand why they changed it to a shitty sounding one around 200
and we all know about the massive use of the original recorded chorus in '87, but there were quite a few occasions where Jon sounded dreadful and it wasn't saved by a back-up sound (Tokyo '08 broadcast, Munich 2011 etc).
I can't see him having much of an autotune technique on his microphone thought. I actually don't even know how that should be possible in real-time, but I'm not a technician on that part. However, IF there was this chance and he wanted to take advantage of it he would've exaggerated it to counteract his singing in mid/late '13 since that was out of tune half of the show.