Nasdaq agreed to pay the fine without admitting or denying the allegations, and without further apology.



"The settlement is another important step forward and follows the commission's approval in April of our plan to accommodate investors," Nasdaq OMX CEO Robert Greifeld said in a statement. "In the last year, we have carefully reviewed these events. As market leaders, we view our experiences as opportunities to learn and improve. As part of our commitment to continually improve, we have met with many market participants, engaged leading consultants and closely examined the way we execute initial public offerings."

A few weeks after the botched offering, Greifeld appeared on CNBC and apologized to investors. "We have been embarrassed, and certainly we apologize to the industry," Greifeld said.

(Watch the interview.)

Facebook's IPO on May 18, 2012, was marred by technical glitches that left the market makers—who facilitate trades for brokers and are crucial to the smooth operation of stock trading—in the dark for hours as to which trades had gone through.

Nasdaq said its systems had been "tested extensively" before the IPO but that the testing did not reveal the "design flaw" that caused the glitches.

(Read More: Time to 'Defriend' Facebook?)