The Gloucester star criticised Owens for his handling of Samoa's 13-5 defeat to South Africa, which saw the Pacific islanders eliminated from the Rugby World Cup.
Fuimaono-Sapolu questioned Owens' neutrality on the basis that Wales stood to benefit from a South Africa victory.
Tournament officials have charged Fuimaono-Sapolu with a "breach...of the World Cup disciplinary programme and for alleged infractions of the...terms of participation".
The charge from Rugby World Cup Limited follows a formal warning that was issued to the Samoa Rugby Union in relation to previous Twitter comments from Fuimaono-Sapolu.
The 30-year-old had blasted the International Rugby Board for "unfair treatment" after Samoa were forced to play for the second time in four days.
Fuimaono-Sapolu then compared Samoa's treatment to slavery, the holocaust and apartheid.
"The charge follows a previous formal warning issued to the Samoa Rugby Union, regarding social media conduct by the same player during Rugby World Cup 2011," tournament officials confirmed.
Fuimaono-Sapolu's case will be heard by the independent judicial officer Jeff Blackett, from the Rugby Football Union, on a date still to be confirmed.
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