A campaign to change the moniker of the Palace of Westminster structure had been backed by most MPs and leaders of the Conservative, Labour and Liberal Democrat parties.
A spokesman for the Commons commission said: "The House of Commons Commission welcomed the proposal to rename the clock tower Elizabeth Tower in recognition of HM The Queen's Diamond Jubilee, and will arrange for this decision to be implemented in an appropriate manner in due course."
"They have agreed to the suggestion and all that remains now is to work out the details with the Palace of when the renaming will happen," a Westminster official told the Evening Standard.
Prime Minister David Cameron's spokesman added: "[It's] a fitting tribute to the Queen and the service she has given to our country in this Jubilee year."
The queen was said to be touched and moved by the original proposal, which came from Conservative MP Tobias Ellwood as an early day motion.