WASHINGTON—A subsidiary of Goldman Sachs pleaded guilty on Thursday and agreed to pay more than $2.9 billion in a foreign corruption probe tied to the Malaysian 1MDB sovereign wealth fund, which was looted of billions of dollars in a corruption scandal. In addition, several current and former top executives at Goldman will have to return millions of dollars in pay and bonuses to the company, a financial penalty for those in charge when the scandal unfolded. Goldman Sachs Malaysia entered the plea in federal court in Brooklyn. As part of its plea, the company admitted that it “knowingly and willfully” conspired to violate U.S. anti-bribery laws. The $2.9 billion includes payments to U.S. and overseas regulators. The penalties also include roughly $600 million in profits Goldman made off the 1MDB scandal that it will have to disgorge. Goldman had previously reached a $3.9 billion settlement with the government of Malaysia. …