This change of heart means Benitez will be able to give all of his first team squad a run out in the Reds' pre-season friendlies, starting at Wrexham next week.
"The Football Association are delighted to announce that FIFA has agreed to the FA's proposal that restrictions on substitutes from friendly matches should apply to international friendly matches only," said an FA spokesman.
"This follows a series of discussions between the FA and FIFA in which the concerns of English football were brought to FIFA's attention.
"The FA believed it was in the interests of all parties that clubs be able to use as many substitutes as necessary in pre-season preparation matches.
"As a result, from this point forward, clubs will once again be permitted to make an unlimited number of substitutions in friendlies."