France were leading 20-16 but Itoje's score, awarded by the television match official and then converted by Owen Farrell, extended their 16-year-wait for a win over England at Twickenham.
Victory saw reigning champions England bounce back from their 40-24 defeat by Wales last time out.
It took France just two minutes to score the opening try of the match through star scrum-half Antoine Dupont.
England, however, hit back through Anthony Watson's try before two penalties from captain Owen Farrell saw them into a 13-7 lead.
France responded with a Matthieu Jalibert penalty before the fly-half converted Damian Penaud's try to give Les Bleus a 17-13 lead at half-time.
Jalibert and Farrell exchanged penalties early in the second half before Itoje powered his way over late on.
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