Boyle: Between God and Science (Yale) was awarded the £2,000 prize and a specially commissioned medal at a special dinner held at St Paul's School, at which Pepys was a scholar, last night (25th October).
Robert Boyle was one of the key figures in the scientific revolution of the 17th century and a founding member of the Royal Society, but was also conflicted by doubts about faith and conscience during his life.
The judges were unanimous in their decision. Chair of judges, Ann Sweeney, described it as a "tour de force". She added: "This is a fascinating portrait of a remarkable man whose strong religious beliefs were balanced by his constant search for explanation in the world of science."
The biennial Samuel Pepys Award is awarded to a book which makes the "greatest contribution" to the understanding of the famous diarist, his times or his contemporaries in the interest of encouraging scholarship in this area.
The first winner of the prize was Claire Tomalin's Samuel Pepys: The Unequalled Self published in 2003 to mark the tercentenary of his death in May 1703, with Frances Harris, John Adamson and JD Davies also previous winners.