The gold is Fourcade's second Olympic medal; he won silver in the mass start event in Vancouver. The Frenchman also holds five world titles, including two in the pursuit discipline.
"Before today, I had already won more than I expected to win my whole life," Fourcade said. "I will just go on now and keep trying to win more titles. It's crazy."
The victory confirmed Fourcade's dominant season. He has won four World Cup events and leads the overall standings by 121 points over Norwegian rival Emil Hegle Svendsen.
Svendsen finished seventh in the pursuit, 40.2 seconds behind the Frenchman.
Fourcade was a strong favorite in the sprint that opened the Olympic biathlon competitions Saturday, but he came up well short to finish sixth.
But he needed less than a kilometer on Monday to join up with the leaders of a pursuit race that started tight. He only missed one target, the second in his third round of shooting, but his fast skiing easily made up for the time lost during his circuit of the 150-meter penalty loop.
Jean-Philippe Le Guellec of Canada briefly grabbed the lead after the second round of shooting, but the tip of his left ski later broke after he slipped and fell head-first during a sharp right turn.
Rain had set in just before the race on a warm day in the mountains above Sochi, which made for difficult conditions. Several athletes slid off the course at the point where Le Guellec fell and broke his ski.
After winning Saturday's sprint, Bjoerndalen opened Monday's race and led after the first round of shooting. However, he missed one target in each of the three following rounds and had to ski an extra 450 meters in penalties.
While Bjoerndalen came just short of finishing third, he has several more chances — including two relays with the strong Norwegian team — to win the 13th medal that would put him one ahead of cross-country skiing great Bjoern Daehlie.
Bjoerndalen didn't feel he wasted an opportunity to overtake his fellow Norwegian on Monday.
"No absolutely not," Bjoerndalen said. "I do my race, and I wasn't strong enough on the shooting. I had three misses and that's too much."