Holmes was elected Fellow of the Royal Society (FRS) in 2000, and Fellow of the Australian Academy of Science in 2006. In 2003, he received the Descartes Prize and in 2012 the Royal Medal of the Royal Society. His formal titles include Chemistry alumnus, Laureate Professor of Chemistry, University of Melbourne; CSIRO Fellow, CSIRO Division of Materials Science and Engineering; Emeritus Professor and Distinguished Research Fellow, Imperial College London; Fellow of the Royal Society; Fellow of the Australian Academy of Science; Fellow of the Australian Academy of Technological Sciences and Engineering; and Foreign Secretary and (as of 2014) President of the Australian Academy of Science. In 2011, he received the Royal Society of Chemistry's John B Goodenough Award.
In 2004 he was appointed a Member of the Order of Australia "for service to science through research and development, particularly in the fields of organic synthesis and polymer chemistry"; and in 2017 was appointed Companion of the Order of Australia for eminent service to science through developments in the field of organic and polymer chemistry as a researcher, editor and academic, and through the governance of nationally recognised, leading scientific organisations. He was awarded the 2021 Matthew Flinders Medal and Lecture.