The Rohan-Rutuja duo struggled in the initial set of the match and lost the first set against Chinese Taipei's En-shuo Liang and Tsung-hao Huang by 6-2.
It was a mixed day in office for Indian tennis players in the season-opening Australian Open with Sania Mirza sailing into the third round of the women's doubles event even as Rohan Bopanna crashed out of the men's doubles, here.
Fourth seeds Sania and her Czech partner Barbora Strycova eased past the Australian-Chinese pair of Samantha Stosur and Shuai Zhang 6-1, 6-4 in one hour 21 minutes in a second round duel.
The Indo-Czech combination, who finished runners-up at last week's Apia International in Sydney, will next play Japanese pair of Eri Hozumi and Miyu Kato.
However, it was curtains for Bopanna in the men's doubles event and he and his new partner Pablo Cuevas of Uruguay were knocked out by unseeded Australian pair of Alex Bolt and Bradley Mousley in the second round.
Bopanna and Cuevas, seeded 15th, lost 6-2 6-7 (2) 4-6 to their unseeded opponents in one hour and 55 minutes to put an end to the Indian challenge in the men's doubles competition.
Veteran Leander Paes and his partner Andre Sa of Brazil, as well as the all-Indian pair of Purav Raja and Divij Sharan have already made first round exits from the event.
In the women's doubles encounter, Sania and Strycova came up with a dominant display from the word go and broke their opponents twice to race to a 4-0 lead in the first set.
Stosur and Zhang managed to break Sania's serve once to reduce the margin to 1-4 but the Indian-Czech pair broke back and went on to pocket the first set from their third set point.
In the second set, Sania once again conceded her serve in the second game to trail 0-3.
But Sania and Strycova got their acts together in time and won three straight games to level the scores at 3-3.
The Indo-Czech pair then broke their opponents with a forehand volley to take a 5-4 lead and serve for the match.
But Sania and Strycova were made to work hard by Stosur and Zhang as the Indo-Czech duo had to save five break points and needed four match points to win the final game that lasted over 13 minutes.
Bopanna/Cuevas and Bolt/Mousley exchanged three service breaks in the opening three games of the first set, Bopanna and Cuevas winning two of those to lead 2-1. They held serve twice and then broke serve once again before serving out the set, winning 28 points to 19 for their opponents.
Bopanna and Cuevas pocketed the first rather easily to seize the initiative.
But the second set turned out to be more competitive and proceeded on serve. However, Bopanna and Cuevas faltered in the tiebreak as Bolt and Mousley went 5-2 ahead with two forehand winners.