Prior to crashing after running wide off the track at Turn 13, Lynn was under little pressure in a race that was dramatically shortened thanks to a long red-flag period caused by first-lap shunts.
The red flag was caused by four cars crashing at the long Turn 3 left-hander on the opening lap.
Russian Time driver Artem Marklov ran wide at the second corner, hitting the wall on the left-hand side of the track as he attempted to rejoin, suffering a front-left puncture and shedding his rear-left wheel.
Vandoorne: I had to dominate GP2
That meant he spun as he returned to the track, which led to Marlon Stockinger and Sergio Canamsas having to go wide in avoidance and ending up in the barriers.
All three cars ended up in the barrier at the same point.
Jordan King also crashed heavily further around the long corner, most likely as a result of front-end damage caused when he clipped the rear of Stockinger under braking for Turn 2.
It was the King shunt that caused the red-flag delay to be so long thanks to the need for barrier repairs, with the delay running to just over 30 minutes.
When the race was restarted with the distance reduced from 28 to 15 laps, it was under the safety car with the order dictated by the brief green-flag period before the accidents.
Lynn, who converted pole position into the lead at the original start after fellow front-row starter Stoffel Vandoorne wheelspun his way down to fifth, executed a perfect restart.
He finished the fourth lap, and the first entirely run under green-flag conditions, 2.7 seconds ahead of Rossi.
Lynn pitted on lap six to switch from the soft-compound Pirellis that most drivers started on, with Rossi attempting to pull enough of a gap to retain the lead before pitting two laps later.
The Racing Engineering driver succeeded, but Lynn was right with him at Turn 2 after Rossi rejoined and took the de facto lead around the outside of Turn 3.
With victory seemingly in the bag as leader Vandoorne still had to pit, Lynn then crashed out on lap 12 and handed the initiative to Rossi.
But the American still had to see off the challenge of Vandoorne, who ran long on the soft-compound Pirellis and pitted on the lap Lynn crashed.
Vandoorne was close, but could not stay ahead of Rossi or the second DAMS entry of PIerre Gasly, meaning he had to settle for third place and could not clinch the title today.
Sergey Sirotkin took fourth ahead of Rio Haryanto, with Raffaele Marciello sixth.
Red Bull-backed Dean Stoneman took ninth on his GP2 debut for the Carlin, finishing just behind Arthur Pic who had taken the restart third but dropped to eighth.
Vandoorne seals GP2 title in Russia
Lynn denies Vandoorne Sochi pole