Waites is a two-time BDO world champion in 2013 and 2016 who has also won the World Masters when it was held in his home county of Yorkshire back in 2011.
But this year's Essex venue almost picked up another famous scalp as Paul Hogan twice went a set up against the No 23-ranked player.
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However, 'Crocodile Dundee' has never made it through to the quarter-finals of this prestigious tournament and as nerves kicked it, Waites started to find his rhythm, levelling the match at two sets all to force a decider.
The 42-year-old hit his straps at exactly the right time and took the final set 2-0 to set up a clash with Carl Hamilton in the quarter-finals.
In the other half of the draw, John O'Shea "finally showed up" to roar past Willem Mandigers, ending the last remaining Dutch involvement in the tournament.
With seeds falling left, right and centre, it looked as though No 7 Mandigers would buck the trend as he raced through the first three legs.
However, O'Shea won his first leg of the game with a 147 checkout and an enormous celebration, which the Irishman said altered the whole complexion of the contest.
"I showed up - eventually. Finally, John O'Shea showed up," O'Shea said.
"The 147 changed the whole game. It gave me everything I needed to push on.
"I play the game with my heart on my sleeve and I just wanted to play well."
O'Shea recorded the highest average in a winning effort of the whole week - 97.25 - and won six of the last seven legs to book his place in the next round.
Earlier in the evening, 20-year-old Ciaran Teehan took to TV darts with ease as he brushed aside Roemer Mooijman to move into the quarter-finals to add yet more of an Irish flavour to the last eight while Michael Warburton beat Keith Geraghty to make sure Wales would have a representative on Sunday.
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