As a result, Romelu Lukaku's hat-trick and Adnan Januzaj's debut will be wiped from the records.
The Belgium coach made five alterations at half-time in Genk to give his players some game-time ahead of the World Cup, and the sixth change saw Divock Origi replace Lukaku just after the hour.
Sides are only permitted to use six substitutions in friendlies under Fifa regulations, which were broken when Nicolas Lombaerts was introduced in the 77th minute.
"This match has subsequently been declared unofficial due to Belgium exceeding the maximum number of substitutes permitted," Fifa confirmed on Wednesday.
The decision means Januzaj will have to wait until Saturday's tie against Tunisia to earn his first official international cap, having not been used in Belgium's 2-0 victory over Sweden on Sunday.