The 27-year-old left the final shooting stage 20 seconds behind her Russian opponent but she made her move on the final uphill to take victory in 28:05.40minutes, with a single penalty.
Starykh, who shot clean, took silver 4.2seconds behind, while Tiril Eckhoff of Norway was 15.5secs back in third for the first podium result of her career.
Gabriela Soukalova of the Czech Republic was fourth but she tops the overall World Cup standings after seven competitions, with Starykh in second and Switzerland's Selina Gasparin, winner of Saturday's 7.5km sprint and sixth in the 10km, in third.
Semerenko said: "I did not expect such success here in France. It is a nice New Year present to myself.
"I am happy to win, especially after such a battle with a great competitor like Irina on the last lap. It is just starting to sink in now."
Meanwhile Johannes Thingnes Boe proved that Saturday's maiden World Cup victory was no fluke as he made it two wins from two in impressive style in the 12.5km men's pursuit.
The Norwegian again dominated proceedings, clocking a time of 31:43.70mins with one penalty, to finish 37.5secs ahead of clean-shooting Erik Lesser of Germany while Anton Shipulin took bronze for Russia.
It means the 20-year-old junior world champion becomes the youngest ever winner of a World Cup pursuit race, leaving him third in this season's overall World Cup standings, although Martin Fourcade remains out in front on 306 points.