Nadal confirmed he would return to pole position for the first time in over two years after he was handed a free pass to the Beijing final following a back injury to semi-final opponent Tomas Berdych.
Berdych retired 4-2 down in the first set, after running for a backhand, to continue Nadal's unbeaten run since his shock first-round exit to 135th-ranked Steve Darcis at Wimbledon.
It also set up the chance for Nadal to claim an 11th title of the year - an unlikely achievement after he returned from seven months on the sidelines with a knee problem in February.
"(This is) a great year, one of the best years of my career without any doubt," Nadal was quoted as saying on the ATP Tour's official website.
"(It) sure is special be back to the top position of the rankings after more than a half year without playing tennis.
"I worked hard every day with the right attitude I think, and because of that, I am today in this situation. I am number one today, but it's not (assured) for the end of the season.
"I (won't) go to sleep tonight feeling that I am the best player of the world. That's something that I never thought, and I don't - think (that) now today. I played a very complete season, and that's why I am the best in the rankings today.
"If I am able to be number one at the end of the season, then, that's an important achievement because I will be the best of the year - that's something that really motivates me."
Djokovic will stand in his way of another title, however, after he overcame an early break of serve to beat fifth seed Richard Gasquet 6-4 6-2 in an hour and 20 minutes.
The Serbian will spend the last day of his 101 weeks at the top before Monday's rankings confirm his fall, no doubt keen to exact some revenge on Nadal.
"I know (on Sunday) I am going to have a very tough opponent," Nadal said.
"I need to play my best, playing aggressive, playing without mistakes, being solid with my serve. If these kind of things are not happening, I will not have chances.
"I know what I have to do [but] it's very difficult to do it, because the level of the opponent is unbelievable."
In the women's draw, top seed Serena Wiliams will meet Jelena Jankovic in the final.
Williams coasted past Agnieszka Radwanska 6-2 6-2 while eighth-seeded Jankovic stormed to victory after losing the first set to Petra Kvitova 6-7 (9/7) 6-1 6-1.