The pair exchanged vows in Westminster Cathedral on Saturday in front of a small group of close friends and family.
He is the first prime minister to marry in office since Lord Liverpool married Mary Chester in 1822.
On Sunday, Downing Street confirmed that the wedding had taken place.
“The Prime Minister and Ms Symonds were married yesterday afternoon in a small ceremony at Westminster Cathedral,” a Number 10 spokesman said:
“The couple will celebrate their wedding with family and friends next summer.”
The couple’s guests were invited at the last minute - with even Tory aides unware that the nuptials were going ahead.
The Sun reports that the church was cleared shortly after 1.30pm, with staff telling visitors it was being closed due to lockdown.
Ms Symonds arrived at the church at 2pm. She wore a white dress but no veil while Mr Johnson wore a “very dapper” suit.
The ceremony was carried out by Father Daniel Humphreys, who baptised the couple’s one-year-old son Wilfred last year.
Armed police were said to be standing by for the ceremony.
One witness said the cathedral was closed for the half-hour service. They told The Sun: “It’s not very often we have weddings here, and when they came out they were all bungled into a car.”
Mr Johnson and Ms Symonds were the first unmarried couple to live in Downing Street. They live in the four-bedroom residence at No11 Downing Street rather than the smaller flat in No 10.
The couple got engaged in December 2019 while on holiday in Mustique.
It is Mr Johnson’s third wedding - and Ms Symonds’ first.
The prime minister married Allegra Mostyn-Owen in 1987, but that marriage was annulled in 1993 — the same year he married Marina Wheeler.
Mr Johnson and Ms Wheeler had four children but separated in 2018.
Their final divorce came weeks before the news of Mr Johnson’s engagement to Ms Symonds.
Weddings in England are currently subject to strict coronavirus restrictions.
Dancing is discouraged due to the increased risk of transmission. The traditional first dance between bridge and groom is permitted.
Vaccines minister Nadhim Zahawi offered his congratulations to Boris Johnson and Carrie Symonds following their wedding.
“It’s a great feeling as you come together and of course I think it’s a wonderful thing for both of them, that they have made their marriage vows to one another,” he told Sky News.
Northern Ireland’s First Minister Arlene Foster tweeted: “Huge congratulations to Boris Johnson & Carrie Symonds on your wedding today.”
Cabinet minister Therese Coffey sent her congratulations to the couple “on your marriage”.
Minister for children and families Vicky Ford sent her congratulations and “big love to Wilf”, adding: “So many weddings have been delayed and disrupted by covid. Life is always better with love,”
The wedding comes at the end of a difficult week for the Prime Minister in which his former aide Dominic Cummings branded him unfit for office.
The Prime Minister’s former aide said Ms Symonds had been desperate to oust him from his role, and had sought to put her own friends in key positions.
Mr Cummings also claimed that in February 2020, when the pandemic was becoming a major global crisis, Mr Johnson was “distracted by finalising his divorce.