In 1939, ten years after work ceased at St. Marys, a team of scientists at the Sir William Dunn School of Pathology at the University of Oxford, led by Howard Florey that included Edward Abraham, Ernst Chain, Norman Heatley and Margaret Jennings, began researching penicillin. Their starting point was Flemings largely forgotten paper and a sample of penicillin mould Fleming had given to their laboratory in 1930. They developed a method for cultivating the mould and extracting, purifying and storing penicillin from it, together with an assay for measuring its purity. Chain hit upon the idea of freeze drying it, which enabled the water to be removed, resulting in a dry, brown powder. They carried out experiments with animals to determine penicillin's safety and effectiveness before conducting clinical trials and field tests. They derived its chemical structure and determined how it works. The private sector and the United States Department of Agriculture located and produced new strains and developed mass production techniques. During the Second World War penicillin became an important part of the Allied war effort, and is credited with saving the lives of thousands of soldiers.
When the news of the curative properties of penicillin broke, Fleming revelled in the publicity. Journalists told a familiar story of a lone British scientist and a serendipitous discovery. The British medical historian Bill Bynum wrote:
In 1943, the Nobel committee received a single nomination for the Nobel Prize in Physiology or Medicine for Fleming and Florey from the British biochemist Rudolph Peters. The secretary of the Nobel committee, Göran Liljestrand, made an assessment of Fleming and Florey in the same year, but little was known about penicillin in Sweden at the time, and he concluded that more information was required. The following year, there was one nomination for Fleming alone and one for Fleming, Florey and Chain. Liljestrand and Nanna Svartz considered their work, and while both judged Fleming and Florey equally worthy of a Nobel Prize, the Nobel committee was divided, and decided to award the prize that year to Joseph Erlanger and Herbert S. Gasser instead.
In 1945 there were a large number of nominations for Florey and Fleming or both, and one for Chain, from Liljestrand, who nominated all three. Liljestrand noted that thirteen of the first sixteen nominations that came in mentioned Fleming, but only three mentioned him alone. This time evaluations were made by Liljestrand,  and , who endorsed all three. The Nobel Assembly at the Karolinska Institute considered awarding half to Fleming and one-quarter each to Florey and Chain, but in the end decided to divide it equally three ways. On 25 October 1945, it announced that Fleming, Florey and Chain equally shared the 1945 Nobel Prize in Physiology or Medicine "for the discovery of penicillin and its curative effect in various infectious diseases."