Amazonian Lass ($10) scored a short-head win from Zardozi with Harlow Mist ($5) a further 2-¼ lengths away third.
Waterhouse and Bott won the 2017 Oaks with Pinot while Waterhouse's solitary win in the Wakeful Stakes came with Tuesday Joy in 2006.
The filly was stepping up to 2000m on Saturday after Waterhouse said the three-year-old was one-paced when third behind Zardozi in the Group 2 Edward Manifold Stakes (1600m) at Flemington on October 7.
"She's a very big filly, big hindquarter, very strong and she did it really well today," Waterhouse said.
"I know she was being threatened in that last furlong, but I just love that courage she's got.
"We've just kept the work up to her since her last run.
"I think people often think when you say keeping the work up to her means you've got to be hard on them, but it is the consistency.
"And she's worked very well, she eats very well, she's gone to the beach.
"She's just a happy horse."
Waterhouse hopes Amazonian Lass will remain a happy horse until the Group 1 VRC Oaks (2500m) on Thursday where she will join stablemate Tropical Squall in the filly's staying Classic.
Clark said the team in Melbourne looking after Amazonian Lass had been confident the filly would enjoy the rise in journey to 2000m on Saturday.
"She's been going great, the team have been really happy with her down here," Clark said.
"There is no reason not to turn up here again Thursday, as that'll top her off nicely.
"She's got a wonderful attitude and I'm sure she'll run a hell of a race Thursday."
