Oxford University academics have rejected reforms proposed by the vice-chancellor which could have handed financial control to outsiders.
Dr Hood said he now wanted to put aside division
Dr John Hood had wanted to change the 900-year-old tradition of Oxford's self-governing council and bring in external members to oversee finances.
But a postal ballot of Oxford's parliament rejected the proposals by 1,540 votes to 997, a majority of 543.
Dr Hood said in a statement that he intended to stay on as vice-chancellor.
His plans took a knock when members of the ruling body voted 730 to 456 against them after a three-hour debate at the university's Sheldonian theatre.
The proposals then went to the postal ballot of the nearly 4,000 members of the university's parliament of dons.
Dr Hood said the proposals had reflected more than two years of debate and consultation and he had supported them because he believed they served the best interests of the university.
"However, members of congregation have taken a different view, first at the end of the debate in the Sheldonian theatre last month and now in the postal ballot.
"That view, twice expressed, deserves to be respected," he said.
He added: "We shall fare best if we are able to work collegially on the basis of mutual trust and respect.
"That is a central task for any vice-chancellor and it is why, in my recent letter to all members of congregation, I wrote: 'whatever the outcome of the postal ballot, I assure you that I will want to do all I can to put aside division, continue dialogue with all shades of opinion, and in an atmosphere of trust, tolerance and goodwill, promote the academic aims and ideals of Oxford."
Dr Hood, a former businessman from New Zealand, had wanted to alter the make-up and responsibilities of the university's council
There are currently 25 members of the council - including four lay members - responsible for both academic and financial matters.
Dr Hood wanted to replace this with separate academic and financial boards.
His proposal was for the council running the university's financial affairs to be composed of seven external and seven internal members plus a chairman - who would be the chancellor, Lord Patten, for the first five years.
After that, an existing external member of council would have become chairman.
A compromise amendment agreed by 652 votes to 507 on November 14 made it possible for the replacement council member to be an internal candidate.
However, critics said that the internal majority would include the vice-chancellor and the representative of Oxford's colleges - so Dr Hood would still have effective control.
Oxford's parliament - the Congregation - voted on this amended proposal at the university's Sheldonian theatre on November 28 following a three-hour debate and nearly 30 speakers.
However, since the theatre could accommodate no more than 1,200 of the 3,700 members of the parliament the postal ballot was held.
Lord Patten has said that without reforms it will be harder to raise private money that the university needs to support students from poorer backgrounds.
But opponents feared such reforms threaten to undermine the ancient university's academic standing and want university insiders to retain control on the council.
Queen's College fellow Nicholas Bamforth, who had opposed the plans, said the issue had never been about personality and he would not expect Dr Hood to stand down.
He said changes did need to be made and he hoped that the council could discuss the best way forward in the new year.
"Clearly people don't want disruption but I am sure that there are all sorts of useful things that could be taken forward," he said, adding: "We're thoroughly in favour of outside advice but we're not in favour of outside control."