Amid mounting criticism of the decision to include Sami Khiyami on the invitation list, Foreign Secretary William Hague decided the day before the ceremony that his presence would not be "acceptable".
His invitation, when Britain is at loggerheads with Damascus over the bloody crackdown on protesters against President Bashar Assad, had sparked fury, particularly among Labour supporters angry that former prime ministers Tony Blair and Gordon Brown were omitted from the guest list.
In a statement, the Foreign Office said representatives of all countries with which the UK had diplomatic relations had been invited.
"An invitation does not mean endorsement or approval of the behaviour of any government, simply that we have normal diplomatic relations with that country," it went on.
"In the light of this week's attacks against civilians by the Syrian security forces, which we have condemned, the Foreign Secretary has decided that the presence of the Syrian ambassador at the royal wedding would be unacceptable and that he should not attend.
"Buckingham Palace shares the view of the Foreign Office that it is not considered appropriate for the Syrian ambassador to attend the wedding."
The ambassador said he found the withdrawal of the invitation "a bit embarrassing" but he was not surprised or disappointed.
"I find it a bit embarrassing but I don't consider it a matter that would jeopardise any ongoing relations and discussions with the British Government," he told BBC Radio 4's The World At One.
Asked whether he understood the controversy surrounding his invitation, he said: "Well, I don't really understand it, but I understand the influence of media on government decisions."
The withdrawal of the ambassador's invitation came soon after former Foreign Secretary Jack Straw said the authorities should have found a way to ensure he did not attend.
Mr Straw said he believed a way could have been found to avoid the attendance of Dr Khiyami, who was summoned to the Foreign Office on Tuesday to receive a dressing-down over his government's handling of protests.
Dr Khiyami's invitation sparked anger because of the bloody crackdown on protests, which are believed to have left as many as 500 civilians dead and even reportedly prompted mass resignations by members of President Assad's ruling party.
Mr Straw also described himself as "surprised" that Mr Blair and Mr Brown were not invited to the wedding, adding: "I certainly think the former prime ministers should have been."
But Mr Blair said he did not mind missing tomorrow's wedding.
Speaking during a visit to Colombia, Mr Blair said it was "not a problem at all" and wished Prince William and Kate Middleton every happiness.
Asked in an interview for Colombian TV whether he was upset not to have been invited to the wedding, Mr Blair responded: "Absolutely not at all."
Mr Blair said he was "delighted" for the royal couple and thought it was "completely sensible" for them to invite people from different walks of life, rather than politicians, to tomorrow's ceremony.
Downing Street said that Prime Minister David Cameron agreed with Mr Hague's decision that it would not be appropriate for the Syrian envoy to attend, but played down suggestions that it amounted to political interference.
"It is a family wedding, not a state occasion," said a Downing Street spokeswoman. "The guest list has been compiled by the couple and the royal household.
"Regarding foreign countries, it is right that the Foreign Office has discussions with the palace."
She added: "The British public have seen what has happened in Syria and probably agree that the Foreign Secretary's decision is a good one."
She refused to be drawn on whether the move reopened questions about other countries' representatives attending the wedding.
Bahraini pro-democracy campaigners were mounting a vigil outside Saudi Arabia's embassy in London today to protest against the invitation to Prince Mohamed bin Nawaf bin Abdulaziz, following the Saudi military intervention in their country.
Human rights protester Peter Tatchell, who is joining the demonstration, demanded the withdrawal of the invitations of royals from seven countries, including Saudi Arabia.
Mr Straw said: "My guess is that, reviewing the way the guest list has worked, in retrospect I think the decision-makers probably would have made some different decisions, both in respect of former prime ministers and in respect of the number of ambassadors being invited."
A spokesman for St James's Palace said this week that there was no protocol reason to invite Mr Blair or Mr Brown.
"It is a private wedding and the couple are entitled to invite whoever they want to it. Prince William is not the Prince of Wales or the king and he hasn't got that link to prime ministers in the way that the Queen does," the spokesman said.
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