Richard Anderson, 57, who was dismissed from Boston grammar school shortly after the incident on November 11, had his appeal against the governors'
decision partially upheld. He will return to school in January providing he abides by conditions that have not been disclosed.
John Neal, the headteacher, closed the school on Thursday and Friday last week after reading on the internet about plans for a pupil protest against the dismissal of the popular head of German.
Mr Neal told The TES: "Closing the school was probably a drastic measure but we did not want to put pupils and staff at risk. While I regret the incident and the distress caused to the pupil and his family, I am also pleased that I have a colleague who can resume his career."
During the alleged incident Mr Anderson ordered an unruly Year 9 boy out of the classroom and asked him to take his bag with him. When the boy walked out without his bag Mr Anderson is understood to have thrown the bag towards him. He denies aiming the bag at the boy or trying to hit him with it. The boy claimed the bag hit his head and hurt his neck. He returned to school in a neck brace.
Asked on Radio 4's Today programme if he regretted using such force, Mr Anderson said: "I didn't use a lot of force but I just wanted to make a noise to make it obvious that I was not best pleased."
He admitted that his behaviour had been at fault as well as the Year 9 boy's.
The Conservatives this week called for accused teachers to be granted anonymity, but were defeated in a House of Commons debate.
Tim Collins, shadow education spokesman, MP for Westmorland and Lonsdale, described the case of David Sowerbutts, a retired headteacher who lives in his constituency.
Mr Sowerbutts was arrested for rape and indecent assault after a woman claimed he had attacked her nearly 30 years ago, but the case collapsed.
Mr Collins said: "My constituent was branded a paedophile, spat at in the street, had his home vandalised and worst of all, received a series of terrifying death-threat calls telling him every day for a week to kill himself or get ready to be murdered."
Stephen Twigg, education junior minister, said the Government had introduced stricter press protocols to reduce the likelihood of teachers being publicly identified before they were charged.
He added that it was trying to speed up cases involving teachers. A study of 1,600 such cases this year by the Department for Education and Skills found that most were resolved quickly but that one in 10 took up to a year or longer.