Arriving at York Minster Cathedral, the women were greeted by Eugenie's husband Jack Brooksbank - who was one of the groomsmen at A-list nuptials of the British popstar and art dealer Caspar Jopling.
The trio's rare appearance comes as Prince Andrew continues to face backlash over his relationship with late sex criminal Jeffrey Epstein.
Buckingham Palace has declined to comment on the new photos, which have only drawn further attention to the questionable past associations of the Queen’s second son.
Despite the scandal, Fergie and her daughters were in high spirits as they joined celebrities including singer Katy Perry and her Hollywood star boyfriend Orlando Bloom at Ellie's big day.
Prince Harry's ex-girlfriend Cressida Bonas, singer James Blunt and actress Sienna Miller were also there.
Ellie wore a traditional bespoke wedding gown with a veil and train designed by Natacha Ramsay-Levi for Chloe, while Mr Jopling opted for a suit from Savile Row tailors Huntsman.
The pair exited the minster after tying the knot, pausing on the steps to kiss before descending amongst a crowd of friends and family.
The 32-year-old Brit Award winner and her husband then left in the same blue Volkswagen campervan that delivered them to the service on Saturday afternoon.