Rufus promised his then fellow trustees at the Kingsway International Christian Centre (KICC) an annual return of 55%, the commission said - but in reality the charity lost £3.9 million as a result.
The 41-year-old, who played more than 300 games for Charlton, was declared bankrupt in 2013 in the wake of investigations by financial authorities.
Last year, a specialist civil court judge branded him a fraudster, saying he had "exploited trust and friendship" after running a Ponzi-like scheme which left investors millions of pounds out of pocket.
Rufus, a Christian, resigned as a trustee of the charity and the trustees who gave him the money between June 2009 and June 2010 without seeking independent advice first have also stood down.
A Charity Commission investigation into the affair has now finished and KICC's new trustees have agreed that their predecessors' "decision to invest was not a prudent or reasonable one".
The charity now has an investment manager and new guidelines.
In a statement the Charity Commission's director of investigations, monitoring and enforcement, Michelle Russell, said: "This case is a reminder that trustees must ensure that they do not permit any personal associations to interfere inappropriately with their judgement as charity trustees and that any decisions they make are in the best interests of their charity.
"We make clear in our policy and guidance that where trustees are reckless and make poor decisions that are not in the best interests of the charity and result in significant losses, the commission will ensure that they are held to account.
"It was appropriate that in this case the charity pursued restitution to recover or repay the losses against the trustees who made these decisions."
KICC is famous for being one of the largest churches in the UK by congregation number, with thousands regularly attending on Sundays.
In a statement the church said: "The current trustees accept the Report of the Commission and acknowledge the seriousness of the decision that was taken by the former trustees seven and a half years ago. The trustees at that time believed they were acting in the best interests of the charity and have not benefitted personally.
"None of the current trustees were involved in the decision making regarding the investments with the now ex-trustee. Since then, we have worked with the Commission, and our professional advisors, to put robust controls in place that would prevent any reoccurrence.
"With the benefit of hindsight it is clear that the former trustees' decision to invest was not a prudent one but was done in good faith. The Charity has since continued to operate and successfully carry out its charitable objectives to the community and looks forward to continuing to do so."
