After reaching the final five times and losing every time - three to Federer - Djokovic jumped and punched the air in celebration of his breakthrough.
The older man looked poised to take the opener when he was presented with two break-point and set-point opportunities in the 12th game, but Wawrinka dug deep to save the first with a forehand down the line, before staving off the other by coming to the net and forcing Federer to send a forehand passing shot long.
"It's been a rollercoaster week with matches and the interruptions with the rain and all that's happened", Djokovic said.
Novak Djokovic overcame a battling Marin Cilic 6-4 3-6 6-3 to reach his sixth Cincinnati Masters final on Saturday while Roger Federer enjoyed a less-taxing route to the title match after his semi-final opponent David Goffin retired with a shoulder injury. Then, it was off for a little rest before play Wawrinka, the second match of the day for both players.
Djokovic leads their all-time series 24-22, doing better in the biggest matches.
Despite pulling double duty, Cilic got the better of Carreno Busta in what was a lengthy first-set tiebreaker, finally clinching it on his fourth set point.
Federer, who has won all seven of the finals he has appeared in at the ATP Masters 1000 event, had taken the opening set 7-6 (7-3) and it was 1-1 in the second when 11th seed Goffin was forced to call a halt to the contest. It was very, very tiring, the second set, and I just think that I couldn't really find energy in the third one.
"For sure it's completely different than last week".
"Definitely Novak is playing really well". Last week were really important and really good for myself, for my tennis, for my confidence. "I've now got a hard final against a tough opponent".
Del Potro is facing 11th-seeded Belgian David Goffin, a 6-2, 6-4 victor over sixth-seeded South African Kevin Anderson in another rain-delayed match.
"I am happy to be winning some matches". He's 3-1 against Federer in Grand Slam finals and 12-6 overall in championship matches, including wins at Wimbledon and the U.S. Open in 2015. I think we're all a bit mentally and maybe physically exhausted but I'm looking forward to this final. Seventeen hours later, she was back on court and needed only 5 minutes and eight points to complete the 4-6, 6-3, 6-3 win Thursday afternoon.
On Sunday she'll try again against Dutch outsider Kiki Bertens, who will be playing her third final of the season after wearing down a tiring Petra Kvitova 3-6, 6-4, 6-2.
"But I've found out that I need to have the game B in the end of the day".