Rattled by the opening day's singles defeats, India went with experienced players, leaving out Vishnu Vardhan, who was initially named to play the doubles along with Bhuapthi.
India are still trailing 1-2 and need to win both the reverse singles on Sunday with Somdev Devvarman clashing with Kei Nishikori and Bopanna taking on Sugita.
Although both Bopanna and Bhupathi play the left court, the Indian captain did not want to risk fielding Somdev, who encountered a shoulder problem during the opening match against Sugita, on Friday.
Sugita and Ito do not feature in even top-450 in the doubles ranking chart but they tested Bhupathi (6) and Bopanna (14) to limits, forcing them to come out with their best effort as the match lasted three hours and six minutes.
Indians played well in patches and consistency was not there. The Japanese were all fired up and gave their best. Ito specially, served extremely well while Sugita never failed to raise his level when his team required him to do.
India nosed ahead in the opening set on Sugita' serve when Bopanna's forehand winner earned them third breakpoint and Bhuapthi's backhand winner converted it in the third game.
The Indian pair faced two breakpoints in the next game with Bhupathi serving but no damage was done.
India let go the advantage of initial break as Bhupathi was broken in the eighth game, which allowed Japan to level the score 4-4 and then failure to convert three breakpoints put the hosts ahead 5-4.
However, India managed to break Sugita in the 11th game and then Bhupathi served out the set to take a 1-0 lead.
Ito was successful in holding his serve after saving a break chance in the opening game of the second set but Bopanna was not that lucky as he went down 0-40 in the sixth game and the hosts converted second point to go ahead 4-2.
That break proved costly for the Indians as the next three games went with serve and Japanese restored parity.
The Indians woke up and raised their level by a few notches and claimed the third set by breaking Sugita twice even as Bhupathi surrendered his serve in between.
More the Indians put the Japanese under pressure, the better played the hosts, who opened up a 4-1 lead in the fourth set by yet again breaking Bhupathi early.
India saved a set point on Ito's serve in the ninth game and then after squandering two break chance converted the third to reduce the trail margin to 4-5.
Eventually, the set was decided through tie-breaker, in which the Indians prevailed.