Brazilian forward Lucas struck twice with
Yasuyuki Konno and
Masato Morishige scoring one each for the west Tokyo team's first success in the season-closing tournament.
Tokyo, which will play in the first division next season after winning the second division, began the game at a fast pace against its second division counterpart.
But it was Kyoto that found the net first when midfielder
Hiroki Nakayama picked up a loose ball to cut inside the box and fire home in the 13th minute.
Tokyo equalised two minutes later when Japan defender Konno headed in a cross from
Tokyo, marshalled by former Japan midfielder
Naoyuki Hanyu, took the lead in the 36th minute as Morishige added the finishing touch following an Ishikawa free-kick.
Lucas made it 3-1 with his 42nd minute strike from close range.
Kyoto tried to rally after the break with good efforts from 19-year-old attackers
Yoshinari Komai and
But Tokyo added a fourth in the 66th minute as Lucas scored his second from a tight angle to give his team a 4-1 lead.
Kyoto did not give up and went close with efforts from
Takayuki Fukumura and
Jung Woo Young.
It was rewarded in the 71st minute when Kubo headed in from a Jung corner. The Korean midfielder also hit the bar in added time.
"We played the game as we wanted to play, to some extent, and Hanyu took the pace to put pressure on to our opponents," Tokyo's out-going manager Kiyoshi Okuma said.
"I had a strong desire to take this team to Asia. I'm grateful to our players to make that happen.
"I always felt it important that a team from a capital city competes in the world, and you cannot do that if you cannot reach Asia to feel the distance from the rest of the world. I knew our players are capable of doing that.
"I hope they can get stronger next season and retain the tournament."