John Womersley will step up from his position as director of science programmes at the STFC to become chief executive on 1 November after Keith Mason stood down five months ahead of schedule.
Professor Mason, who has been seconded to the UK Space Agency, was heavily criticised by the Commons Science and Technology Committee for presiding over a "leadership vacuum" that had contributed to a fractious relationship between the council and academics.
Many of the scientists whose concerns about Professor Mason were quoted in the committee's report into astronomy and particle physics, published in May, welcomed Professor Womersley's appointment.
Robert Kennicutt, Plumian professor of astronomy and experimental philosophy at the University of Cambridge, said the former director of particle physics at the Rutherford Appleton Laboratory was "highly respected" among astronomers.
"During the turmoil of the past couple of years, he was a steady voice of reason in the organisation, and his common-sense approach helped to defuse some of the tensions that had arisen between Professor Mason and the scientific community," he said.
"Clearly the challenges he faces ahead as chief executive will dwarf anything he had to face as the director of science programmes and, for that reason, I suppose some observers will withhold their judgement. But nearly everyone I know welcomes (his appointment)."
George Efstathiou, professor of astrophysics at Cambridge, said Professor Womersley had "an understanding of academic research, which his predecessor sadly lacked".
He added: "Under (Professor) Mason, the STFC swung drastically towards a simple-minded impact agenda. The real argument is much more subtle and went well over his head. It is not just about spin-offs and supporting industry. Research in particle physics and astronomy is primarily about the intellectual strength and depth within the UK. This has an impact over the entire scientific spectrum."
Michael Bode, director of the Astrophysics Research Institute at Liverpool John Moores University, agreed that Professor Womersley had been "a central figure in re-establishing the trust of the community" and was "ideally placed to take up the reins very rapidly".
Others to welcome the appointment included Paul Crowther, professor of astrophysics at the University of Sheffield, who said he was "both pleased and relieved" by the decision.
Professor Mason will spend the remainder of his five-year term, which was due to end on 31 March 2012, advising the UK Space Agency on how to "leverage the research base to maximise the economic growth of the space sector".
Andrew Miller, chair of the Science and Technology Committee, said: "I know we have crossed swords over a number of issues but I wish him well."