World number one and defending champion Djokovic prevailed 6-3, 6-2, 3-6, 6-2 in a bizarre semi-final that saw 10th-seeded Monfils roundly booed and accused of not trying.
Third-seeded Wawrinka withstood an early onslaught from sixth-seeded Kei Nishikori of Japan, asserting himself in the later stages to claim a 4-6, 7-5, 6-4, 6-2 victory.
Although Djokovic holds a 19-4 record over Wawrinka, including two victories since the Swiss player shocked him the French Open final last year, Wawrinka welcomed the chance to take him on again.
“To play Novak again it will be very special,” he said.
Djokovic admitted he was “completely caught off guard” when Monfils, down 0-5 in the first in 15 minutes, stood lackadaisically in the court and began chipping the ball back.
The strategy paid off as Monfils reeled off three games in a row.
“If I would get to the net he would go for the passing shot and hit some impossible gets and balls. But that’s Gael,” Djokovic said.
It was Djokovic who emerged with the set, however, and as the Serbian star raced through the second Monfils’s interest again appeared to wane.
By the sixth game the 30-year-old had won just nine points, which he managed to nudge into double figures by the end of it.
Monfils, playing in only his second Grand Slam semi-final after making the last-four at the 2008 French Open, theatrically hobbled off the court and was jeered.
He was booed again by sections of the 20,000-strong crowd as he dropped the first game of the third set.
Monfils said his tactics were a deliberate attempt “to get inside his head”.
A more orthodox approach saw Monfils break back for 2-2 and again for 4-2 in a third set that saw Djokovic receive treatment on his left shoulder.
Although Djokovic saved one set point, and gave himself three break chances in the ninth game, Monfils was able to extend the match, marking the moment with a mighty roar to which Djokovic responded by ripping off his shirt.
“I think I should not have allowed him to come back to the match after two sets to love up and 2-love in the third,” Djokovic said.
“He started believing in himself. I think the crowd disliked his efforts towards the end of the second set. I think he felt like he needs to step it up and start to play better, which he did.”
After giving back an early break in the fourth Djokovic had treatment on his right shoulder, but he broke twice more to close out the win.
Djokovic arrived at the semi-finals having played just two complete matches in five prior rounds after a walkover from one opponent and the mid-match retirements of two others.
Wawrinka’s arduous path to the title match included saving a match point in the third round.
He’s spent 17 hours and 54 minutes on court.
Nishikori, coming off his own five-set quarter-final triumph over world number two Andy Murray, seized the initiative with a near flawless first set.
He broke Wawrinka again to open the second, but the Swiss was gradually beginning to find his range and regained the break.
After saving a bevy of break points, he broke in the 12th game to level the match at two sets apiece.
After taking the third and breaking Nishkori at love for a 2-0 lead in the fourth, Wawrinka appeared to be on his way.
Nishikori’s last gasp was a break in the fifth game, but a quick break back and a hold at love and Wawrinka was back in charge.
“He dictated play early tonight, put pressure on me and gave me no time,” Wawrinka said.
“I had to wait and fight and make him uncomfortable. He got tired and I started to be more aggressive.”
Wawrinka, who was in the US Open semis for the third time in four years, was delighted to finally make it to the final.
“I am really excited,” he said. “I have seen the final here on TV many times, watching Roger, Rafa, Novak.”
Nishikori, meanwhile, was denied a chance to improve on his runner-up to Marin Cilic in 2014.