"Both applications are dismissed," Special CBI Judge O P Saini said, adding the "trial will continue as it is".
The court had reserved its order on the pleas after hearing arguments of CBI and the counsel for ETHL and a private firm's director, facing trial in the 2G case.
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ETHL, which is facing trial in a case arising out of the probe into the 2G spectrum scam along with the promoters of Essar Group and Loop Telecom, had moved the court seeking a joint trial with former Telecom Minister A Raja and others in the case.
The private firm director Rajiv Agarwal, facing trial with former Telecom Minister A Raja, too had moved a similar plea.
Earlier, CBI had opposed the pleas saying any "attempt to derail the trial" would be against the Supreme Court's order of day-to-day proceedings.
Special Public Prosecutor U U Lalit had argued no prejudice would be caused to the accused if the trial was conducted separately in the case.
Senior advocate Harish Salve, who had appeared for ETHL, said CBI has created a "mess" and a "big confusion" has been created due to their stand.
He had said CBI had told the apex court that section 220 of CrPC (trial for more than one offence) would apply in the case while before the trial court, they have argued that it would not apply.
Regarding CBI's arguments that 146 prosecution witnesses have been examined in A Raja's case and 71 witnesses have recorded their statements in Essar-Loop case, Salve had said ETHL was just demanding its right.
"If you have persuaded and told the Supreme Court that section 220 of CrPC will apply and that I have been made an accused in 2G scam, 146 or 1,460 witnesses will not matter. I am demanding my right. I will not go to any other court," he had said.