The 20-year-old, who competes under a Dutch licence, infringed three virtual safety car procedures in Saturday's race at le Castellet and was handed three points for each infringement.
Added to the points he already had, Raghunathan reached the 12 point limit that triggers an automatic ban, meaning the Chennai-born driver will miss next weekend's round in Austria.
The MP Motorsport driver has yet to score a point this season.
In April he was given a 10-place grid penalty after he took the chequered flag twice at the Bahrain season-opener, continuing at racing speed for an extra lap after the finish.
(Reporting by Alan Baldwin, editing by Nick Mulvenney)
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