Fans turned up before sunrise in the cobbled streets around Windsor's town hall, Guildhall in the city of London, where Prince Charles and Camilla Parker Bowles wed in April.
John and Furnish strode into the building for the ceremony at about 10.50am, pausing briefly to smile and wave at the cameras.
Andrea Lever, who travelled more than 300km from Torquay in southwest England for the event said: "It's a special day for Elton. I want to be a part of it really, it's good fun and it's interesting to see what's going on."
Suzi Uprichard, 33, of Maidenhead, was excited to take part in what she described as a historic day for same-sex couples.
"It's a long time coming really," Uprichard said. "Admittedly, it's Elton and David's day, but it's the first day that gay couples can engage in civil ceremonies in ... England. So I think it's something to celebrate."
Police erected security barriers outside the sturdy building of brick and Portland stone partly designed by Christopher Wren, but expected no trouble.
Relaxed officers, some on horseback, chatted with photographers, who stood four and five deep on the streets outside Guildhall in the city of London.
Windsor police spokeswoman, Sue Mahoney, said: "It's not a major police operation - it's not a royal wedding, the general atmosphere seems to be jolly, very good humoured."
Fans got into the spirit of the event with posters featuring the couple and Queen Elizabeth II.
A nearby shop wished the couple well with handpainted sign saying "go for it".
John and Furnish are the most prominent of hundreds of same-sex couples planning to form civil partnerships in England and Wales on Wednesday, the first day that such ceremonies become possible.
The new law is seen as a landmark
for gay couples
Ceremonies were held earlier this week in Northern Ireland and Scotland.
Three couples signed their documents moments after the register office opened at 8am in Brighton, the south coast city known as Britain's gay capital.
Gino Meriano, who was with his partner Mike Ullett said: "I'm really excited, I'm very happy to be one of the first."
Gay rights activists see the unions as joyous - and important in advancing efforts to give same-sex couples the same rights as heterosexuals.
Gay love profile
Peter Tatchell, spokesman for the gay and lesbian human rights group OutRage! said the wedding "would raise the profile of gay love and commitment.
"Their same-sex civil partnership ceremony will be reported all over the world including in countries where news about gay issues is normally never reported.
"This will give hope to millions of isolated, vulnerable, lesbian and gay people, especially those living in repressive and homophobic countries."
"This will give hope to millions of isolated, vulnerable, lesbian and gay people"
Furnish, a Canadian-born filmmaker, and John have been together for 12 years.
The couple plan a low-key private ceremony, with only John's mother and stepfather and Furnish's parents expected to attend.
The reception, by contrast, is expected to be a star-studded extravaganza costing an estimated $1.75 million.
Guests at the couple's bachelor night on Monday - a prelude to the bigger reception on Wednesday - included heavy metal rocker turned reality TV star Ozzy Osbourne and his wife Sharon, model and actress Liz Hurley and musicians Bryan Adams, Gary Barlow and Kid Rock.
The new law - passed last year despite some opposition from parliament's unelected House of Lords - allows civil ceremonies that will give same-sex couples the same social security, tax, pension and inheritance rights as married couples.
However, it has met opposition from some conservative religious groups who say marriage should be restricted to a union between a man and a woman.