The pair had cited personal reasons for not wanting to link up with Paes at the London 2012 games.
Now Bhupthi, 38, and 32-year-old Bopanna have been excluded from the competition until June 2014 by the All India Tennis Association.
The AITA decided at its executive committee meeting to continue with the young team in its Davis Cup matches, AITA secretary-general Bharat Oza said in a statement late Saturday.
"It is further decided not to consider Mahesh Bhupathi and Rohan Bopanna for selection to play for India till June 30, 2014," he said.
Bhupathi tweeted in response: "The cranky old grand fathers on the executive committee, who have never played tennis waiting for a reaction? There is one coming. stay tuned!"
The controversy over the Olympics team selection started after the AITA had initially named Bhupathi and Paes for the doubles, even though Bhupathi wanted to play with his current partner Bopanna.
The AITA were later forced to pick two doubles teams for the Olympics, with Paes pairing with lower-ranked Vardhan, and Bhupathi partnering Bopanna.
The selectors last month axed Bhupathi and Bopanna for the ongoing Davis Cup Asia-Oceania Group I tie against New Zealand in Chandigarh and named a new-look team comprising Yuki Bhambri, Vishnu Vardhan and Divij Sharan.
The youngsters have already taken an insurmountable 3-0 lead in the ongoing tie.
Paes and Bhupathi had formed a long-standing and highly successful team for years, winning Grand Slam doubles titles at the French Open in 1999 and 2001, and Wimbledon in 1999 as well as representing India at four Olympics in the doubles.
They broke up as a full-time pair in 2002, but continued to team up for India in the Davis Cup and other multi-sports tournaments such as the Olympics and Asian Games.