He was one of seven people in the running for the V.S. Pritchett Short Story Prize, an annual award organised by the Royal Society of Literature that received more than 1,000 entries, and was announced as the winner at a ceremony in London.
Dr Vowler won for his work Voyagers, which follows two female astrophysicists on a psychedelic journey exploring love, illness and the cosmos.
Author and judge Julia Armfield described it as being "clean and balanced, combining science and romance with flair and intelligence", while judge Fred D'Aguiar said it was a story "with real intrigue and knowingness that makes compelling reading".
The prize was open to authors of unpublished short stories of between 2,000 and 4,000 words, and was founded in 1999 to commemorate the centenary of the renowned 20th-century author.
As the winner, Dr Vowler received the first prize of £1,000 and Voyagers has also now been published in Prospect magazine.
