Ireland's Cian O'Connor and Netherlands rider Gerco Schroder had to take part in a jump-off for the silver and bronze medals.
Schroder took silver and O'Connor secured Ireland's first medal of London 2012 with the bronze.
O'Connor, riding Blue Loyd 12, gave it everything, clocking a faster time than Schroder in the jump-off, but he had one fence down.
Schroder's horse, aptly called London, almost helped Netherlands deny Great Britain the Team Jumping gold two days ago, but he will leave for home with two silvers.
Ireland failed to qualify a team for London 2012, and were restricted to two Individual places.
Great Britain's Nick Skelton, the last rider to go, would have forced a jump-off with 30-year-old Guerdat.
I told my wife last night I was going to get in and jump a good round and she said 'dream on'.Cian O'Connor
But one fence down - the first his stallion Big Star has had in six rounds of Jumping across Team and Individual competitions in London - cost him a medal.
Guerdat said: 'It's difficult to explain how I feel. I did not know when I came out after the second round if I had a medal or not.
'Then with two riders left I knew I had a medal and then I felt bad for Nick when the fence went down, so I will just enjoy it now.
'I am just happy for myself and my team. I am proud but I am more happy for the people behind me. They have helped me so much as a team and this gold medal is theirs, not mine.'
O'Connor added: 'I told my wife last night I was going to get in and jump a good round and she said "dream on". So many people have put a lot of work in for me to get here. It has been a wonderful journey.'