The Qatar Stock Exchange tumbled eight percent on opening and eventually closed down 7.58 percent.
Cairo has accused Al-Jazeera of supporting the Muslim Brotherhood which it blames for violence after Egypt's military ousted the movement from power in 2013.
Bahrain blamed Qatar's "media incitement, support for armed terrorist activities and funding linked to Iranian groups to carry out sabotage and spreading chaos in Bahrain" for its decision.
"There is a wider impact than Qatar Airways not being able to land in markets like Saudi and UAE since those markets are significant sources for transfer traffic", said Will Horton, a senior analyst at CAPA Centre for Aviation in Melbourne.
Less than a month ago, US President Donald Trump visited the region to cement ties with powerhouse Saudi Arabia - the first foreign stop of his young presidency.
U.S. Secretary of State Rex Tillerson urged the Gulf nations to resolve their differences.
Qatar is home to three U.S. airbases and plays a role in collective defense efforts for the region.
In a statement issued on Sunday, Qatar's ministry of foreign affairs said: "Qatar has been exposed to an instigation campaign based on allegations that amounted to absolute fabrications, which proves that there are premeditated intentions to cause damage to the State".
The dispute between Qatar and the Gulf's Arab countries started over a purported hack of Qatar's state-run news agency.
Doha denied the comments and said it had been the victim of a "shameful cybercrime".
Gas-rich Doha, which has long exercised an independent streak in its foreign policy, last month denied comments which appeared on its official news agency questioning United States hostility towards Iran.
Kuwait and Oman, however, did not embrace the Saudi decision to isolate Qatar.
Trump nevertheless met with Qatar's emir during the Saudi conference last month.