By Jonathan Stempel

Jan 30 (Reuters) - A federal judge ordered an end to the U.S. Securities and Exchange Commission's 16-year-old lawsuit over Allen Stanford's $7.2 billion Ponzi scheme, directing the financier and two former colleagues to pay sums that will go largely uncollected.

In a decision on Wednesday, Chief Judge David Godbey of the Dallas federal court imposed a $5.9 billion civil fine on Stanford, who is serving a 110-year prison sentence after being convicted in 2012 of defrauding about 18,000 investors.

Godbey ordered Stanford Financial Group's former chief financial officer James Davis to pay $17.66 million, including a $5 million fine, and former chief accounting officer Gilberto Lopez to pay $3.42 million over their roles in the fraud.

Authorities said Stanford sold fraudulent high-yielding certificates of deposit through his Antigua-based Stanford International Bank during a two-decade fraud, and used investor money to make risky investments and fund a lavish lifestyle.

The judge also deemed billions of dollars owed by various Stanford entities satisfied by court-appointed receiver Ralph Janvey's recovery of more than $2.5 billion for fraud victims, including $1.2 billion from Toronto-Dominion Bank TD.TO.

Godbey said there was "no just reason for delay" in ordering the payments and closing the case.

Once considered a billionaire, Stanford was declared indigent in 2010. Now 74, he is ineligible for release from prison until 2103.

Lawyers for Davis and Lopez did not immediately respond to requests for comment. An SEC spokesperson declined to comment.

Davis was the top government witness at Stanford's trial, testified against his former college roommate, and was sentenced in 2013 to five years in prison. Lopez was convicted separately, and sentenced in 2013 to 20 years in prison.

The SEC sued Stanford in Feb. 2009, two months after the late swindler Bernard Madoff was criminally charged with running a much larger Ponzi scheme.

(Reporting by Jonathan Stempel in New York. Editing by Mark Potter)

((jon.stempel@thomsonreuters.com; +1 646 223 6317; Reuters Messaging: jon.stempel.thomsonreuters.com@reuters.net))