The Serbian claimed the first set 6-1, but Del Potro responded with a 6-3 success to force a decider, which went to a tie-breaker.
Djokovic eventually emerged victorious 7-3, but the 26-year-old has insisted that it had been an "even match".
"He's a fantastic player and a great person. He showed that again. He has a really likable personality [and] he's a big fighter," Djokovic said during his post-match press conference.
"All the way up to the last point, I didn't know if I was going to win the match. It was a very even match. My motivation is there always, especially when I'm playing finals of such a big event."
The victory earned Djokovic around £450,000 in prize money.