Gerco Schroder of the Netherlands, riding London, and Cian O'Connor of Ireland, on Blue Loyd 12, jumped off for silver with Schroder going clear to take second place after O'Connor hit the top rail of the final fence. O'Connor won the bronze medal.
Schroder had scored 1 time fault in the first round and O'Connor 1 time fault in the second.
"He can jump anything if I ride him good," Guerdat said of his horse after his clean first round. "He feels fresh, like he could jump five more rounds."
Ian Millar of Perth, Ont., a 10-time Olympic medallist, finished tied for ninth while defending gold medallist Eric Lamaze of Schomberg, Ont., failed to make the final round.
"I think my mare is tired. She has jumped a lot of big courses here and she hasn't a lot of experience," Lamaze said. "I did not wake up this morning imagining myself on the podium so I am not too sad."
O'Connor returns to the Olympic medals podium after finishing first in individual show jumping in Athens in 2004. However, his horse there tested positive for a banned substance and he had to return the medal and serve a three-month suspension.
There were two British riders among the last three to ride, raising expectations that a local rider might take a medal. But Nick Skelton, on Big Star, and Scott Brash, riding Hello Sanctos, both dropped one rail each to finish tied for fifth with Mexico's Alberto Michan on Rosalia la Silla.
A field of 22 riders advanced to the second round from the 35 who started the day. Riders from the first round could incur no more than 5 jumping and time faults to advance. Three rounds of qualifying earlier in the games started with 75 horse and rider combinations.
The United States, which won team gold and individual bronze in Beijing in 2008, had only one rider still in the competition for the last round. Rich Fellers, riding Flexible, carried 5 faults forward and had a clean second round to finish eighth.
The other U.S. rider to start the day, McLain Ward, had three fences down on Antares to count 12 faults and did not advance.
Ian Millar of Canada, riding in his 10th games, a record for any athlete, knocked down a rail in each round on Star Power to finish tied for ninth.
In show jumping, fences knocked down or refused by the horse count four faults, plus faults are accumulated for exceeding the time allowed.
The British riders won team show jumping gold on Monday, and three of their riders made it into the final round.