d'Espagnat is troubled by the scant attention paid to philosophy of physics
Bernard d'Espagnat, a French physicist and philosopher, has won the annual Templeton Prize with a purse of £1m.
The prize honours "an exceptional contribution to affirming life's spiritual dimension" and has been awarded to scientists and theologians.
Professor d'Espagnat, 87, worked with great luminaries of quantum physics but went on to address the philosophical questions that the field poses.
The award will be officially presented by the Duke of Edinburgh on 5 May.
The prize is consistently the largest annual award given to an individual.
A professor emeritus from University of Paris Sud, d'Espagnat told BBC News that he would use one-third of the prize money to fund the kind of research he has pursued, and will donate a further third to charity.
The Templeton Foundation award is largely designed to honour work that finds a common ground between science and religion, with the award going more often to scientists than theologians or philosophers.
Professor d'Espagnat's scientific pedigree put him at the centre of the growth of quantum mechanics, working with Nobel laureates in the field including Enrico Fermi and Niels Bohr.
But he was troubled by how little the field was addressing the philosophical questions raised by the theory - which for the first time suggested that experiments were not measuring an absolute reality and that the experimenter could influence the result.
While Professor d'Espagnat's work is not explicitly religious, he aims to delineate what science cannot definitively rule out.
His concept of an ultimate reality - as he terms it, "the ground of things" - is only glimpsed, not explicitly described, by science.
Science, he said, "is aimed not at describing 'reality as it really is' but at predicting what will be observed in such-and-such circumstances".
"What science really teaches us is that it's not with ordinary concepts that we shall ever reach 'the ground of things'," he added.
The spiritual, he argues, cannot be ruled out by scientific endeavour. However, for him, the existence of something inexplicable does not create an uncomfortable sense of mystery.
"Mystery is not something negative that has to be eliminated," he said. "On the contrary, it is one of the constitutive elements of being."