According to reports the couple then went on a mini-moon at the seaside and are expected to have a more traditional getaway and a bigger party planned for 2022.
Asked about the funding of his wedding, a spokesman for No10 said: "The Prime Minister paid entirely for the wedding."
It comes after the PM was embroiled in a row over the funding of a lavish refurbishment of the No11 flat he shares with Carrie Symonds - who has taken his surname.
Downing Street also said Mr Johnson spent Sunday and Monday away after the private do, but declined to say where he went.
The spokesman said: "The PM spent Sunday and Monday away but is now back working from Downing Street."
Asked where Mr Johnson travelled, the spokesman said: "It is a personal matter so I won't be getting into any further detail.”
The wedding is said to have even caught Downing Street aides by surprise and Mrs Johnson reportedly rented three "decoy" dresses to ensure maximum secrecy around the event.
Mrs Johnson apparently rented three extra dresses from ecofashion business My Wardrobe HQ - thought to be of differing colours in order to throw people off the scent.
The dress she wore and the three decoys were delivered to Downing Street a few days before the wedding, The Times reports.
"We didn't know what it was for," Sacha Newall, who co-founded My Wardrobe HQ in 2018, told the paper.
"We were just asked to supply some items. Then we saw what happened this weekend. It was all a bit of a surprise."