Djokovic held his nerve, sealing the win on his first match point after just an hour and 25 minutes on court.
"It was a roller-coaster match", added the Wimbledon champion, who admitted he was distracted my loud music coming from outside the court early in the third set.
"That's what the headline should be about - this is such an fantastic accomplishment", Federer said.
Wimbledon champion Djokovic claimed his Masters record on his first match point and now heads to the US Open as a title favorite after several seasons of dismal form and an elbow injury which required surgical intervention. Djokovic leads a rivalry, which dates to 2006, by a thin 23-22 margin with the Serb winning three of their last four meetings. She'd never beaten a top-ranked player, but wore down Halep at the end of her two draining weeks.
Federer's streak of 100 straight unbroken service games in Cincy was ended by Djokovic in the seventh game of the first set. Bertens would break Halep twice more and close out the match with an emphatic ace.
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The set continued to go on serve and at 3-3 Federer took a 40-0 lead before several uncharacteristic unforced errors at the net and on his backhand wing brought it back to deuce.
"I played five finals before, and most of those finals I lost to this great man, Roger. thank you for letting me win here once in Cincinnati", Djokovic joked. However, Djokovic remained steadfast in his relentless defense, leveling the set at 2-2. "If I fight like I've done here, I will have a big chance", Halep said.
"I need a little bit of rest because I'm exhausted", Halep said.
Djokovic only secured his defeat of Cilic late in the final set, breaking for 5-3 and finishing off the hard-fought victory in the next game. "It's a great confidence (boost)".
Bertens is an unexpected finalist, winning only one match during three previous appearances in Cincinnati.
Djokovic has become the first player who won in all 9 Masters.