Just one of the 34 combinations to make it through to the show jumping went clear, with Johnstone taking three rails and Todd two.
Johnstone went into the show jumping knowing a clear round would give him a win in the final, but says it wasn't his ride's day.
"It was a very difficult track," he said.
"The ground was very hard, it was hot and he just didn't jump well."
Johnstone, who was part of the bronze medal-winning team at the world championships in Kentucky last year, ranks this as his most important win.
Meanwhile in Scotland at the Blair Castle International horse trials, New Zealander Andrew Nicholson won the three-star international event on Calico Joe, and finished fourth aboard Shady Grey.
- NZPA