Duncan Kelly and Ray Chiu, who were both scientists at medical devices company Amersham International, which became GE Healthcare in 2004, brought the case.
They co-invented a radiopharmaceutical heart imaging agent. Branded as Myoview, this has had sales estimated at more than £1.3 billion.
Section 40 of the Patents Act 1977 provides that a court may award compensation to an inventor where a patent is of outstanding benefit to the employer.
This was amended in 2005 so that compensation can be paid when the invention, rather than the patent, is of outstanding benefit. However, this case was decided under the old law.
The law has been criticised as vague, and there were no reported cases of successful awards under it until last week.
But in his judgment on April 11, Mr Justice Floyd said that the patents have been of outstanding benefit to Amersham and added: It is just that the employees should receive an award of compensation.
In calculating the award, he said that the employees share of the value of a patent might in principle lie somewhere in the broad range from nil to as much as 33% or beyond. In the present case I think the employees share lies towards the bottom of the scale.
Floyd estimated the value of the patent at £50 million, and awarded the inventors 3% of this amount, though he said both figures were very conservative.
He added that £1 million should be paid to Kelly, and £500,000 to Chiu.
While this is believed to be the first such award in the UK, there have been numerous similar awards in countries such as Japan and Germany.
In Japan, Shuji Nakamuras claim against Nichia over the patent for the blue LED led to a series of similar suits being filed by inventors.
Kelly and Chiu were represented by barristers Iain Purvis QC and Will James, and by Marks & Clerk Solicitors.
GE Healthcare was represented by barristers Henry Carr QC and Andrew Lykiardopoulos, instructed by Bristows.