Pamela Cliffe, whose son Matthew Wilson was alleged to have been violent and disruptive, bowed to pressure after the county council announced it was prepared to act outside its powers to remove him if necessary.
The school was closed last week after its governors decided to stop paying for a supply teacher to look after the boy.
Teachers at the school had voted to strike rather than to teach him after governors at the school overturned the head's decision to exclude him.
His mother was adamant that he should return and had said she would seek a judicial review of the case.
However, her solicitor, Stephen Williams, said yesterday that she was not prepared to see the school remain closed any longer.
Mr Williams said she was "battle weary" after nearly two months of dispute."She feels that no one else seems to have the interests of the children at heart, certainly not the unions or the teachers," He said.
"She feels she has gone as far as she can and is now, reluctantly, going to take him out of the school and make arrangements for him to be transferred elsewhere."
Nigel de Gruchy, general secretary of the National Association of Schoolmasters Union of Women Teachers, welcomed the decision.
"It will be better for the youngster in the long-run. Again, more has been achieved by NASUWT action than all the pious mouthings of politicians about morality," he said. The head teacher, Bill Skelly, shut the school last week on the grounds that he could not guarantee all his pupils' safety, but a staff strike started straight afterwards.
Yesterday he said he hoped the school could return to normal and continue with the task of educating all its pupils.
"School will re-open on Monday and hopefully, the media will respect the right of our pupils to restart their education without the glare of publicity."
Doug McAvoy, general secretary of the National Union of Teachers, which represents Mr Skelley, said it was appaling that the dispute had taken so long to resolve. It first blew up in July, but governors decided to pay for a supply teacher to keep Matthew out of lessons.
"Had the head teacher's judgement prevailed earlier, pupils at Manton school would not have had their education disrupted. Matthew would have had his own educational needs met and the adverse publicity would have been avoided," Mr McAvoy said.
Fred Riddell, chairman of Nottinghamshire education authority, had written to the Secretary of State for Education, Gillian Shephard, asking for her backing if the boy was removed from the school.
Its governing body could not legally reconsider their decision not to exclude him, even though the members who blocked it resigned last week.