Rouen keeper Theo Defourny mishandled Sogou's long-range strike in the 59th minute but appeared to secure the ball before it crossed the line. However, referee Said Ennjimi awarded the goal.
Senegalese striker Sogou joined Marseille earlier this month from CFR Cluj.
Marseille had gone ahead three minutes before the break thanks to Mathieu Valbuena's low shot. Rouen reduced the arrears in the 67th minute when Regis Dugimont beat Steve Mandanda from close range.
The game, scheduled last week, was postponed after a non-toxic gas leak in the Rouen area prompted the French federation to change its plans.
The last-16 games will be played on February 26 and 27.