The Australian star has been involved in each day of the internet-streamed tournament so far this year, but finally tasted victory by seeing off his World Cup of Darts team-mate Nicholson 6-3 in the final.
Whitlock had been the only player to defeat Nicholson during the round-robin league phase of the event on Wednesday at Crondon Park GC in Essex, edging a 6-5 win with an 11-darter in the final leg of that contest.
Whitlock also enjoyed four other wins in the league phase, while Nicholson's win over Dave Chisnall in the final round of matches saw him jump above the St Helens man to finish top of the league table on Legs Won after the pair took six victories apiece.
Whitlock then powered past Chisnall 6-4 in the semi-finals, averaging 107.02 and missing double 15 for a nine-dart finish during a high-quality contest.
He found himself 2-0 down in the final as Nicholson made a strong start, but an 11-dart finish in the third leg kick-started Whitlock's fight.
He then punished four missed doubles from Nicholson to level and produced a 14-darter to lead 3-2 before finishing 121 for a 12-darter.
Whitlock then took out 104 to move 5-2 up, before missing four match darts in leg eight as Nicholson kept his hopes alive by finishing 82 on tops.
Nicholson, though, could not take his chance to stay in the game in the next, as Whitlock posted double ten to claim the win and progress, picking up £2,850 prize money on the day and a place in the big-money Winners Group on November 1.
"I played really well today and I'm very happy with the result," said Whitlock, last month's European Championship winner.
"It was great to finally make a final because I scraped through in a couple of the days, but I've been pretty consistent and all the players seem to produce their best darts here for some reason.
"I was pretty exhausted in the first week because it came just after the European Championship and I scrambled my way through, but I've hit some good form.
"After I lost in the World Grand Prix to Justin Pipe last week, I went home and have been practising really hard and that's paying off for me. I can't wait for the Winners Group in a couple of weeks!"
He added: "It's always hard playing Paul because we're good friends, and it's good to see him playing his best darts again. It's been quite a while since he's played like this and I'm happy he's playing well at the moment."
Nicholson impressed throughout the day to top the league table, and saw off Terry Jenkins 6-3 in the semi-finals to win through to the decider, taking home £2,950 prize money in addition to £1,950 as a semi-finalist in Group Four 24 hours earlier.
He will, though, now have to return for Group Six on Thursday alongside Chisnall and Jenkins, who is the tournament's only ever-present since Group One following Whitlock's success.
Jenkins had sneaked into fourth place with a win over Wayne Jones in the final round of matches as he edged out Robert Thornton for a semi-final place.
Thornton and Mark Walsh join that trio in progressing to play in Group Six on Thursday, with Colin Lloyd and Wayne Jones eliminated after winning just one of their seven games on Wednesday.
Three-time World Champion John Part, 2009 Championship League Darts winner Colin Osborne and Jamie Caven come in on Thursday to complete the Group Six line-up.
Whitlock, meanwhile, joins Wes Newton, Justin Pipe, Ronnie Baxter and Tuesday's Group Four winner Phil Taylor - the reigning champion - in the Winners Group on November 1.