McManus's last win at the World Championship came against Doherty - also in the second round - but he made life difficult for himself after boasting a 10-3 lead at one stage.
Former world champion Doherty won five of the next six frames to put the frighteners on the Scot, who was having trouble stringing together a noteworthy break.
But the 43-year-old Glaswegian set up a clash with world No 3 Mark Selby in the last eight at the Crucible in Sheffield with a majestic 83 to finally seal a 13-8 victory.
Meanwhile, Ronnie O'Sullivan revealed sports psychiatrist Dr Steve Peters was the reason behind his comeback against Joe Perry after prising him away from Premier League champions-elect Liverpool.
O'Sullivan, bidding for his third consecutive World Championship title, was lagging behind world No 15 Perry after the first two sessions before hitting back to tie the match at 11-11.
And two stunning centuries - under the watchful eye of Peters - sealed his place in the quarters as O'Sullivan showed a rare burst of emotion by punching the air.
O'Sullivan credits Peters with helping him clinch his last two World Championship crowns - and his increased presence at the Crucible could spell trouble for the rest of the field.
Peters is also working with Liverpool as they close in on the Premier League title yet O'Sullivan insists it is time to get selfish after coming so close to an early exit in Sheffield.
"I have got friends from Liverpool and it would be so great if they can do it, so I'm mindful that I don't want to take all his time up," said O'Sullivan.
"I said 'that's more important, I'm going to be OK' but really I made a mistake. I could have done with him here on Thursday.
"But he said he's not going to make that mistake again, he's going to be around a bit more now."
After levelling up the scores to one frame each in the first session, O'Sullivan was always behind Perry before reeling him back in with two frames to spare.
And so intense were his last-ditch dramatics that O'Sullivan believes he has never played in a more exciting encounter at the Crucible - including his five previous world-title victories.
"I stayed determined right to the end, I was never going to give in and it was hard coming from behind all the time," said O'Sullivan.
"He was playing really well so every time I got close he pulled away. I was missing a few shots and he got on top of me and I just had to draw on all of my experience.
"I've been here so many times and won a few times so I had to use that as my ace card. That was a more exciting match than any of the finals I've had and my most exciting match at the Crucible."
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