New Zealand veteran Mark Todd was promoted into the lead aboard NZB Land Vision at the end of a chaotic cross-country day at Badminton Horse Trials.
German rider Marina Kohncke's time, which was affected by one of a number of stoppages, was later adjusted to relegate her below Todd into second.
Nicola Wilson leads British hopes in third on Opposition Buzz despite retiring aboard Bee Diplomatic earlier.
Badminton's champion will be crowned after Monday's showjumping finale.
But some of the sport's big British names will be missing - Pippa Funnell withdrew both her horses over the weekend while Oliver Townend was eliminated after a fall on a day on which there were a succession of stoppages.
Sunday's action over the four-mile cross-country course was suspended for the air ambulance to land on more than one occasion, with Germany's Ingrid Klimke and Ireland's Elizabeth Power both taken to hospital having suffered knee damage and concussion respectively. They are believed to be recovering well.
Six horses were retired for refusals, among them Wilson's Bee Diplomatic, overnight leader Ruth Edge's Two Thyme and Emily Baldwin's Drivetime.
A further 12 were eliminated after falls - Klimke and Power joined by the likes of Townend, who fell aboard Ashdale Cruise Master.
Todd initially moved into second place as the last to compete on Sunday, but Kohncke's time penalties were later increased as organisers struggled to accurately assess a number of rounds interrupted by stoppages.
Badminton officials later explained that a miscalculation required two seconds to be retrospectively added to Kohncke's time.
Todd, 55, said: "The horse was great but he definitely got a bit tired towards the end, and I had to nurse him home.
"He's so game and genuine, he kept trying. He picked himself up, I'm delighted with him."
Kohncke, 43, is competing in her first Badminton since 1994 and remains well set for Monday on a horse trained as a showjumper.
"To get going again [after the stoppage] was quite an experience - we've never done that," she reflected.
"But it feels fantastic to come back here to Badminton, I never thought I would.
"Calma Schelly is a showjumping bred horse and she does like to jump, but you never know."
Todd leads with 43.6 points, ahead of Kohncke's adjusted score of 43.8.
Wilson has 44.0 points aboard "absolute joy" Opposition Buzz, on whom she became one of seven riders to post rounds with no time penalties.
"He loves his job. I just worry he's too keen, too strong and makes silly mistakes, and I did have to hold him quite tight," she commented.
Edge - who led the competition following the dressage - retired after horse Two Thyme twice refused, ending her challenge for the Badminton title.
Laura Collett, who topped the standings on Friday on her Badminton debut, lies in sixth place on Rayef behind Piggy French and Jakata, with New Zealand's Andrew Nicholson fourth with Nereo.
Among other British names, Mary King and Imperial Cavalier are seventh while world number one William Fox-Pitt is back in 13th and 17th aboard Navigator and Cool Mountain respectively.
Funnell, who withdrew the slightly lame Redesigned on Saturday, concluded her Badminton involvement for the year by pulling out her other horse, Mirage d'Elle, ahead of the cross-country.
She, like King - who withdrew Apache Sauce - felt the horse was better served being taken elsewhere rather than pressing on, particularly with the firm Badminton ground a consideration.
This year's tournament, which concludes with Monday's showjumping competition, also serves as a key opportunity to qualify horses for the London Olympics in 2012.
While there will be opportunities throughout the year, riders are fighting to qualify horses as soon as they can.
If possible, qualifying more than one horse for the Games ensures riders have at least one back-up if their top horse suffers an injury or loss of form in the year to come.
With five places available on the British eventing team for 2012 and some 15 or more riders in contention, an exceptionally tough battle for selection is expected over the coming months.