Mr Tchenguiz was arrested and questioned in 2011 in a raid on his London headquarters as part of an SFO inquiry into the collapse of Kaupthing bank, one of three Icelandic banks to collapse during the 2008 credit crunch.
But after a judicial review in 2012 the High Court quashed the search warrants and was highly critical of the SFO's conduct.
As a result the SFO was required to pay Mr Tchenguiz and his business entities' costs for those proceedings in November 2012.
In this final settlement the SFO has agreed to pay Mr Tchenguiz £3 million to settle the case and has agreed to pay a further £3 million towards his legal costs within 21 days.
Director of the SFO David Green said: "I am pleased that we have been able to resolve this matter without the need for a costly trial. The SFO deeply regrets the errors for which we were criticised by the High Court in July 2012.
"On behalf of the SFO I apologise to Mr Tchenguiz for what happened to him. The SFO has changed a great deal since March 2011, and I am determined that the mistakes made over three years ago will not be repeated."
Mr Tchenguiz said: "I am happy to accept this settlement from the Serious Fraud Office and bring to a close my disputes with them.
"Whilst I and my business have suffered serious and significant damage at the hands of the SFO, it has become increasingly apparent that the SFO's investigation was influenced by certain third parties, acting in their own commercial interests.
"I have settled my case against the SFO and intend to focus my attentions on those other parties whom I consider are responsible.
"However, I hope that the SFO has learned lessons from this sorry episode."