Shipulin picked up just a single penalty on the shooting range as he crossed the line in a time of 32:11.9 minutes, more than five seconds ahead of his nearest competitor.
Coming in 5.7 seconds back, overall World Cup leader Martin Fourcade finished in second place, while Johannes Thingnes Boe placed third, stopping the clock 21.6 seconds behind the Russian winner.
Sweden's Fredrik Lindstroem was the only clean shooter of the day, with his performance on the range helping him climb from 15th to fourth, 44.7 seconds back.
"It was a crazy competition but I am happy to finish first," said Shipulin. "It was difficult on the shooting range and I really had to fight hard.
"I was scared Martin could catch me in the end, but I am happy I managed to keep him behind.
"I will have to work harder during the summer to keep improving my shooting, so I can be better next season."
With Fourcade leading the way in the overall World Cup standings on 1302 points, Shipulin sits second on 901, while Boe completes the top three on 808.
Read the original article on Eurosport: Shipulin skis to final pursuit victory of biathlon season