Fly-half Kosei Ono's late dropped goal lifted Japan over Georgia 25-22 in rugby at Mikheil Meskhi Stadium on Saturday.
The result comes after Japan won their first ever test in Europe last weekend in Romania
The Brave Blossoms came from behind to draw level at 22-22 with eight minutes to go. Japan were put back on defence then counterattacked 80 metres to set up Ono for the winning points.
Georgia led 9-0 after 12 minutes thanks to penalties by Merab Kvirikashvili. Japan struck back with two penalties to Ayumu Goromaru.
Despite having a man in the sin bin, Georgia laid siege to the Japan line in the minutes leading up to the break, only to see the visitors score a spectacular 95-metre try.
Onozawa started the move with a quick tap penalty close to his line and finished it off two minutes later with Goromaru adding the extras.
The second half started as the first with Georgia taking control of proceedings.
Kvirikashvili added two more penalties and then scored a try and conversion as Georgia made the most of every opportunity that came their way.
But Japan stuck to the task and a third Goromaru penalty in the 56th minute closed the gap to 22-16.
The Japan fullback then added two more kicks to bring the sides level at 22-22 as Georgia struggled with Japan's pace.
The closing minutes could have seen either side grab the victory and in the end it was Japan's defence and the quick thinking of Ono that won the day.
"I've lost one big game through a drop goal but never won one till now," the 52-year-old quipped coach Eddie Jones to Kyodo News in the Georgian capital.
"We showed plenty of courage with the ball in hand and then when we defended without the ball,"
"The mental courage was shown by our desire to attack from our own goal line."
"We were physically out-manned. They were better in the scrums and the line-outs but we still won so it is not a bad achievement," Jones said. "You have got to admire the players."
"We are not physically inferior in terms of size but we are in terms of strength," he told the Japan's website.
Georgia: 15 Irakli Kiasashvili, 14 Irakli Machkhaneli, 13 David Kacharava, 12 Merab Sharikadze, 11 Alexander Todua, 10 Merab Kvirikashvili, 9 Irakli Abuseridze (c), 8 Mamuka Gorgodze, 7 Viktor Kolelishvili, 6 Shalva Sutiashvili, 5 Levan Datunashvili, 4 Giorgi Nemsadze, 3 David Zirakashvili, 2 Shalva Mamukashvili, 1 David Khinchagishvili.
Replacements: 16 Yuri 'Irakli' Natriashvili, 17 Mikheil Nariashvili, 18 David Kubriashvili, 19 Vakhtang Maisuradze, 20 Giorgi Begadze, 21 Giorgi Tkhilaishvili, 22 Lasha Khmaladze.
Japan: 15 Ayumu Goromaru, 14 Toshiaki Hirose (c), 13 Tomohiro Senba, 12 Harumichi Tatekawa, 11 Hirotoki Onozawa, 10 Kosei Ono, 9 Fumiaki Tanaka, 8 Takashi Kikutani, 7 Michael Leitch, 6 Hendrik Tui, 5 Luke Thompson, 4 Hitoshi Ono, 3 Kensuke Hatakeyama, 2 Shota Horie, 1 Yusuke Nagae.
Replacements: 16 Haruki Ota, 17 Takuma Asahara, 18 Hiroshi Yamashita, 19 Michael Broadhurst, 20 Ryu Holani, 21 Atsushi Hiwasa, 22 Yu Tamura, 23 Go Aruga.