"The Church Commissioners are deeply sorry for its predecessor fund's links with the transatlantic slave trade," the organization said in a statement.
The commissioners committed £100 million ($122 million) of investment over the next nine years to "a better and fairer future for all".
The money will target "communities affected by historic slavery", and towards further research about church links to the practice.
Archbishop of Canterbury Justin Welby, the highest-ranking cleric in the Church of England and head of the worldwide Anglican communion, said he was "deeply sorry" for the links.
"It is now time to take action to address our shameful past," he added.
The deputy chair of the Church Commissioners, the Bishop of Manchester David Walker, said the body now hoped to create a "lasting positive legacy".
The Church Commissioners for England was established in 1948 partly with an endowment from Queen Anne's Bounty, a fund dating from 1704 to help poor clergy.
A report it commissioned revealed that Queen Anne's Bounty invested "significant amounts" of its funds in the South Sea Company, which traded African slaves.
It also received donations which were likely to have come from individuals involved in the practice and the plantation economy.
Queen Anne's Bounty funds were subsumed into the Church Commissioners endowment when it was set up. It currently manages a Â£10.1 billion investment fund to support church activities and clergy.
Researchers unearthed the slavery links by combing through ledgers from more than 200 years ago at Lambeth Palace, the Archbishop of Canterbury's official London residence.
"Nothing we do, hundreds of years later, will give the enslaved people back their lives," the commissioners wrote in a foreword to the report.
"But we can and will recognize and acknowledge the horror and shame of the Church's role in historic transatlantic chattel slavery and, through our response, seek to begin to address the injustices caused as a result."
The Church of England has apologized before for its past links to slavery, as Britain reckons with the legacy of its controversial colonial past.
In 2020, it said the fact that some church members "actively perpetrated and profited" from slavery was a "source of shame".
Archbishop of York Stephen Cottrell also called on followers to acknowledge all aspects of the church's past, both good and bad, to make a better future.