The 33-year-old, originally from Brazil but an international with Croatia, had "all but signed" to join the Wanderers as part of the guest player program, but the required approval from FFA was not forthcoming.
Eduardo most recently played for Shakhtar Donetsk last season, playing 41 matches and scoring 18 goals, including one against Sevilla in the Europa League semi-final.
FFA have previously said that the guest player criteria is "a high profile player that not only brings talent and exposure to their market but the entire competition."
With only 15 goals in 11 matches, Wanderers coach Tony Popovic is desperate to sign a high-quality striker and was reportedly furious at FFA's denial.
The Wanderers already have five visa players - the maximum allowed - and were therefore only able to sign Eduardo through the Guest Player spot.
Previously, Eduardo has played at the 2014 FIFA World Cup, EURO 2012 and EURO 2008 with Croatia as well as stints with Arsenal, Dinamo Zagreb and Flamengo.
In August, FFA were criticized for blocking Melbourne Victory's attempt to sign 33-year-old Italian International Alessandro Diamanti.
Diamanti has since joined Palermo in Italy's Serie A where he has captained them eight times this season.
