The Denmark international will undergo an operation on Monday to reset the broken metatarsal that has decimated his campaign.
The 23-year-old had to abort an attempted comeback in January before making his return to action with a 45-minute run-out for the reserves against Manchester United last month.
Agger played an hour for the second string against Bolton Wanderers last week, but continued to complain of pain in his foot.
And, with centre-back Martin Skrtel having become established since his January arrival, the decision has been made for Agger to finally go under the knife to repair the problem.
"It's really bad luck for him," Benitez told the Liverpool Daily Post. "He will be out for three to four months, but he will be back for next season."