An NCLT bench of B S V Prakash Kumar and V Nallasenapathy said, "The waiver is dismissed, the company petition dismissed."
The two firms had sought to challenge Mistry's ouster from Tata Sons last year and alleged that there was mismanagement and oppression of minority shareholders.
They urged the NCLT to use its discretion and waive an eligibility condition for filing such a petition.
The tribunal had held last month that the plea was not maintainable, because the petitioner firms did not meet one of the eligibility criteria prescribed by the Companies Act.
Tata Sons had argued that if preference capital was also considered, the petitioner firms held only 2.17 per cent of the total issued share capital of Tata Sons.
Mistry was removed as Chairman of Tata Sons, the holding firm of Tata Group, one of the country's largest conglomerates, last October.