The brands included D'Cold Total, Corex cough syrup, and Vicks Action 500, among others.
Justice R.S. Endlaw, allowing the 454 pleas filed by the pharma companies, quashed the Centre's notification issued on March 10.
Companies like Pfizer, Glenmark, Procter and Gamble, Reckitt Benckiser, Cipla and others had moved the court against the government decision. The court had granted stay on the notification.
The government had told the court that FDC medicines sold by pharma majors "endanger patient safety".
It had banned the drugs on the ground that they involve risk to humans and hence needed to be withdrawn immediately and contended that safer alternatives were available.
The pharma companies had argued that the ban order was passed without considering clinical data and had termed the government's claim as absurd.