However, justices Ranjana Desai and R V More did not pronounce the reasons in the operative part of their judgement for dismissing the petitions.
A detailed order is likely to be available later.
The petitions seeking CBI probe had been filed in public interest by advocate V P Patil, Mumbai Press Club, Marathi Patrakar Parishad and former scribes S Balakrishna and Ketan Tirodkar.
The Crime Branch of city police is at present probing the case.
Opposing the petitions, Advocate General Ravi Kadam argued that police had already arrested eight members of the Chhota Rajan gang for Dey`s killing, while stringent provisions of the Maharashtra Control of Organised Crime Act (MCOCA) being invoked against them.
Every case need not be given to CBI, he said.
Reacting to the order, Gurbir Singh, President of Press Club, said, "We are disappointed that our petition has been dismissed. Unfortunately, the circumstances remain largely the same--police has caught a couple of small fries and have no idea why and who masterminded the killing. In the interest of J Dey, we would appeal in the Supreme Court".
Senior Counsel Navroze Serwai, appearing for the Press Club, argued that police are yet to nab the main accused in the case and have so far given contradictory reports to the media on the course of investigation.
Dey (56), employed as Editor (Investigations) with English tabloid, Mid Day, was shot dead on June 11 at suburban Powai.
According to the Crime Branch, the eight arrested persons had carried out the murder allegedly at the behest of fugitive underworld don Chhota Rajan.
The judges had earlier gone through the progress reports of the investigations into the case and granted time to the crime branch to probe the killing.
Mumbai Press Club, which has 1200 journalists as its members, filed an affidavit saying that they felt that Dey was murdered due to his professional and investigative reporting into the alleged links between a section of police and members of underworld don Dawood Ibrahim`s gang.
While former journalist Ketan Tirodkar pointed out some instances of alleged nexus between police and underworld and sought to justify a CBI probe into Dey`s murder, another petitioner Balakrishna also made a similar plea saying police probe did not inspire confidence in public.