Djokovic looked tired at times after completing a 2-6, 6-3, 6-4 win over defending champion Grigor Dimitrov earlier Friday.
While Federer narrowly avoided an early exit, another high seed was sent packing earlier in the day as number four Juan Martin del Potro fell to diminutive Belgian David Goffin 7-6 (5), 7-6 (4).
Federer, a seven-time champion here, will be bidding to increase his tournament leading total, while Djokovic is keen to win the only Masters 1000 tournament missing from his trophy collection.
Only a couple of hours later, Djokovic stopped Milos Raonic 7-5 4-6 6-3, improving his career record to a ideal 9-0 against the Canadian.
Djokovic leads a rivalry, which dates to 2006, by a thin 23-22 margin with the Serb winning three of their last four meetings.
Federer has won 14 straight matches in Cincinnati and 17 of his last 18 sets.
"It's great to be back in the finals, against Novak in particular", Federer said.
Djokovic had to come from behind in the first and third sets, and helped seal the victory with a break for 5-3 in the third.
On the women's side, No. 1 Simona Halep will play for the title a second year in a row, facing Kiki Bertens.
Indonesian island hit by another quake, causing landslides
On August 5 hundreds of homes were destroyed in a devastating natural disaster that killed more than 430 people in Lombok . The earthquakes Sunday are in the Pacific Ring of Fire , an arc of fault lines circling the Pacific Basin.
"That's not how I wanted to win, but I'll take it", the Swiss said.
"So I just had to hang tough, not get frustrated, and hope that I was not going to throw in a terrible service game or that he was going to connect perfectly".
The eight-time Olympic gold medallist will train with the Central Coast Mariners for the first time on Tuesday after being granted an open-ended trial with the struggling A-League club, who finished bottom of the 10-team league last season. Halep is seeking her first Cincinnati championship after losing in the finals a year ago and 2015.
Now, it's on to his first Cincinnati final in three years.
"I feel like I'm trying to defend my title from way back when", he said. "So before the match, I'm less nervous than I used to be". He then set out to get his hard-court game in form for the U.S. Open.
Former champion Cilic made his way to the semi-finals with a 7-6 (5) 3-6 6-4 third-round win over Russia's Karen Khachanov before toppling Spaniard Pablo Carreno Busta 7-6 (7) 6-4.
World number 17 Bertens, who played and won two matches on Friday after rain interruptions this week, looked fitter that two-time Wimbledon victor Kvitova in hot, humid conditions. "I really liked, you know, the composure, so to say, the focus that I had all the way through".
Halep has faced the most challenges from the rain, with one match suspended overnight Wednesday and then her third-round match held over for a day as well. 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 hope it's not going to happen again", Halep said. "I was really trying, but nothing". "And that's how I was - in some points I didn't really risk that much and just put it to the court".