The German covered herself with a blanket to avoid the cameras as she left a hotel on the way to the wedding.
The German model was also protected by security guards to prevent waiting photographers from taking her picture.
There were reports the model was booed by onlookers.
She had been staying in a hotel in Lavenham, Suffolk - about 20 minutes' drive from the 14th Century country church where she married Vaughn.
'Uplifting service'
Guests at the service included German tennis champion Boris Becker and Trudie Styler, wife of the rock star Sting.
After the ceremony, Becker said: "It was very beautiful."
Ms Styler said: "It was a very uplifting service. Her dress was very beautiful."
And designer Valentino added: "It was charming. Beautiful."
Journalists and about 200 onlookers were gathered outside St George's Church in Shimpling in the hope of catching a glimpse of the model.
Schiffer's spokesman said of her decision to hide behind blankets: "It's the happiest day of her life. She can be as private as she chooses."
Attempts were made to keep the wedding as private as possible.
There was heavy security at the nearby Elizabethan mansion, which Miss Schiffer has bought and where the couple held their wedding reception.
"I didn't boo but a lot of people did," said Janet Damant, 57, of Ipswich after Schiffer's exit from the hotel.
"The crowd booed because they had waited there a long time to get a glimpse of her and they saw nothing."
Footpath closed
Miss Schiffer, 31, has been with Mr Vaughn for 16 months and the pair invited other celebrity guests including Sir Elton John, Sting, footballer-turned-actor Vinnie Jones, Madonna and her husband Guy Ritchie to the reception at their home, Coldham Hall in Stanningfield, Suffolk.
The footpath running alongside the hall had been closed by Suffolk County Council in an effort to keep the wedding private, annoying local residents.
A council spokesman said it had been done on the grounds of public safety after consultation with police and security men.
Mr Vaughn was best man for close friend Guy Ritchie when he wed Madonna at Skibo Castle in Scotland.
He is not returning the favour, choosing instead his old Stowe schoolfriend Alastair MacIntosh as his best man.
One guest who will not be at the wedding is Man From U.N.C.L.E. star Robert Vaughn.
The 70-year-old actor was widely believed to be Matthew 's father after a relationship with his mother, and had abruptly cut his son out of his life just before his first birthday.
But Mr Vaughn recently revealed that DNA tests had proved he was not Matthew's biological father.
Wealthy
Miss Schiffer, a cover star on 550 magazines in the last 15 years, was previously engaged to magician David Copperfield for six years.
She remains a prominent figure in Germany, helping present the winning bid to host the 2006 World Cup.
The German media constantly speculate she is among the wealthiest German women of her generation, earning an estimated £35,000 per day.
Forbes magazine once put her net worth at about $55m (£38m).