Glasgow's McManus is through to the quarter-finals at the Crucible for the first time since 2005, when he beat Doherty before losing to Ian McCulloch. He is through to the last eight for just the fourth time in his career, having reached the semis in 1992 and 1993.
The 43-year-old's battle against 44-year-old Doherty swung towards the Scot in the second session earlier today as he surged 10-3 ahead, and he was able to complete the job after a late rally from 1997 champion Doherty. Former Masters winner McManus now meets Mark Selby in what is sure to be a match full of high quality tactical play.
Doherty started the final session 10-5 behind, but won the first two frames to boost his hopes of a fight back. McManus had lost four on the spin at that point but he stopped the rot with a break of 67 to go 11-7 up. He could have won the next as well from 43-0 down, but missed the final brown and Doherty potted brown, blue and pink to make it 11-8 at the interval.
McManus dominated the 20th frame, taking it in three scoring visits, then needed just one chance to finish the match, making a composed break of 83.
"Ken really struggled, especially in the first part of the match, it's not the Ken you expect," said McManus. "When he got it back to 10-5 going into the last session, he's still out there fighting so I was never over the line. We're not top players and we both fancied winning the match and in the end I played a little bit better. I was getting nervy because when the winning line presents itself, sometimes it's not easy.
"Against Mark Selby, when I get my chances, I'm going to have to take them because Mark's so used to the big stage. He's one of the premier players in the game without question, I'm going to have to be that bit more consistent and cut out silly mistakes.
"I do like playing the big names. It's a three-session match so I'll go and play three little matches again and see where it takes me. I've got some work to do on the practice table - I'm going to have to go and work for the next couple of days and get my discipline where it needs to be. I'm really looking forward to it - it's a big occasion. There's a lot of guys in this game never get a chance to play in the quarter-finals here."
McManus plans to stick with his tartan trousers and added: "I only brought one pair down. I probably should get a different colour now! It's a bit of fun and adds a little something to the tournament no matter how small it is. I'll keep wearing them because I've not got any choice - it's either them or a pair of denims."
Doherty said: "It was very disappointing. Alan played tremendous match-play snooker. It was long and drawn out at times. Particularly in the second session, I just couldn't get going at all, I just felt absolutely battered and bruised out there - it was a really, really tough game.
"He's one of the toughest match players I've ever faced - he hasn't changed over all the years. His knowledge of the angles and safety was top quality and he just kept me on the back wall all the time. I just didn't have answer for him.
"These chances don't come around that often, but I've enjoyed my time here. It's been thrilling - emotional at times - and I don't want it to be my last time because I love this place so much. It's a fantastic place, it's a great atmosphere - we'll have to wait and see."
Meanwhile, Dominic Dale is in the driving seat of his second round match as he leads Michael Wasley 7-1 (Mark Rawlinson writes).
Wasley recorded one of the biggest first round Crucible upsets in history on Monday by knocking out fourth seed Ding Junhui, but was unable to replicate that kind of form in the opening stages of this match and now has a hill to climb.
Welshman Dale won the opening frame of the match with a break of 74 although Gloucester's Wasley replied with a run of 66 to win the second.
Dale, who is now based in Stroud, won the third by clearing up to the brown with a run of 37 before taking the fourth with a 75 break.
The 42-year-old made a 59 break in the fifth frame, after Wasley was only able to hit 20 earlier in the frame. Breaks of 30 and 40 then saw the reigning Shoot-Out champion win the sixth frame to go 5-1 ahead.
Wasley was first in in frame seven but missed a straight forward black off its spot and was again duly punished by an unforgiving Dale who chalked up the first century of the match, a 106.
The start of the eighth frame summed up Wasley's evening, as he slammed in an excellent long-range red only for the cue-ball to wedge itself in the pack and snooker him on all colours. A tight frame ensued but Dale finally secured it by knocking in a long pot on the final red to secure his sixth frame on the bounce.
The pair will return for the second session of the match at 2:30pm on Sunday afternoon.
