Jankovic beat Russia's Vera Zvonareva 6-2, 6-4, while Kunitsyn survived seventh-seeded Safin's 21 aces to win 7-6 (6), 6-7 (4), 6-3.
The 23-year-old Serb was coming off back-to-back titles at the China Open and the Porsche Grand Prix in Germany.
It was her fourth title this season and the eighth in her career. She was also runner-up twice this season, losing to Serena Williams in Miami and at the U.S. Open.
The No. 9-ranked Zvonareva could not challenge Jankovic in the first set and was broken twice.
After trading service breaks early in the second, Jankovic took a 3-2 lead with a break in the fifth game, but Zvonareva leveled at 4-4 only to be broken again in the ninth game.
Jankovic served and closed the match on her first match point when Zvonareva returned long.
Jankovic, who beat Zvonareva in her two previous events, said she knew she was going to have to work hard for every point.
"I was really expecting a tough match,'' Jankovic said. "I was really focused from the start of the match. I went out there aggressive and really played my game and I was really going after the shots.
"Especially the first set I played quite well. I was dominating. But then the second set my level of tennis went down a little bit and I let her come back into the match. At the end of the second set I focused a little bit and changed the match in my favor.''
Jankovic said she had a difficult year, with many injuries early in the season. But after the Olympics, she said she started to work hard.
"I'm quite close to finishing the year as the No. 1 player in the world, so it's really a huge achievement for me,'' she said.
Jankovic said she is committed to playing in Zurich next week but will then take two weeks off to prepare for the season-ending tournament in Doha.
Jankovic, who was on the top of the WTA Tour rankings for a week in August, took the top ranking from Serena Williams on Monday and will retain it next week because Williams, the runner-up in Moscow last year, pulled out with an injury.
The 71st-ranked Kunitsyn was playing in his first ever ATP Tour final.
Safin, who hasn't won a title since beating Lleyton Hewitt in the final of the Australian Open in January 2005 for his 15th, was playing in his first final since losing to Nikolay Davydenko here in 2006.
Kunitsyn said he had prepared a speech to congratulate Safin on the win.
"I was hoping to win a couple of games and that's it,'' Kunitsyn said. "I still don't know how I was able to outplay Marat, but I guess it happens. I still don't understand how I won.''
Kunitsyn was in control of the match and constantly kept Safin on the baseline. He prevailed in a first-set tiebreaker when Safin made two unforced errors and broke his racket in frustration.
"Had I won the first set it could have gone a different way,'' Safin said.
Safin won five consecutive points on a second-set tiebreaker to stay in the match.
In the third set, Kunitsyn made a decisive break in the sixth game and served out the match at love, closing it with an ace.
"I was chasing him all the time,'' Safin said. "I could not capitalize on my chances. But he converted every time he had a chance and didn't make many mistakes. There's no surprise he won.''
Licht: Where Are The Goals?
Jankovic vs. Dementieva in Kremlin CupВ semis
