The bank said the settlement would reduce its second-quarter net profit by 1.6 billion Swiss francs ($1.8 billion).
The $2.6 billion payment is the highest in a U.S. criminal tax investigation to date, according to U.S. authorities.
"Our reported results for the second quarter and the first half of 2014 were impacted by the resolution of our most significant legacy litigation issue," chief executive officer Brady Dougan said in a statement.
Read MoreEuropean bank CEO pay surges in 2013
"With the final settlement of all outstanding U.S. cross-border matters as announced in May, we brought to a close the most significant and long standing litigation issue for Credit Suisse. I want to reiterate that we deeply regret the past misconduct that led to this settlement and that we take full responsibility for it," he said.
"Obviously there has been some impact, we had to work through it. We certainly appreciate the support we have seen from our customers and a lot of the hard work done by our employees as well," Dougan said, speaking to CNBC.
The group also said it had exited from commodity trading to "further enhance capital and operating efficiencies".
Read MoreSwiss banks apologize for assisting tax cheats
In private banking and wealth management, the Zurich based lender posted a loss of 749 million Swiss francs, driven by the litigation settlement charges. However, the division attracted net new assets of 10.1 billion Swiss francs in the second quarter, the bank said.
"We are working very hard to make sure we have an extremely compliant business, we haven't had any issues on the Libor side, we don't have any material issues in the FX side, but there are are a number of issues that we continue to work through," Dougan told CNBC.
The bank's capital levels, in place for European bank stress tests, slipped to 9.5 percent, falling below the 10 percent threshold and the 11 percent long term target, Dougan said.
Read MoreUBS wealth arm assets near $2 trillion 'milestone'
He said a number of business and real estate dispositions would get the bank above the 10 percent level by the end of the year, as well as organic generation of capital.
"As we said once we get to 10 percent we are going to allocate half of our accretion of capital to distribution to shareholders," he told CNBC.