"I said we are not here to prove something in a court of law. We are here to let them know we know what they are doing and it needs to stop," Crocker told reporters after the meeting, Agence France-Presse reported.
He pointed to an increase in the rate of militant fire into the fortified Green Zone that he said can be traced back to Iran.
According to Crocker, talks with the Iranians at times became particularly heated as the two sides debated where blame for the sectarian bloodshed lay.
"I would not describe this as a shouting match throughout, but we were real clear on what our problems with their behavior was, and I just didn't hesitate to let them know," Crocker told reports, according to Reuters.
But Iranian Ambassador Hassan Kazemi Qomi said the United States has no proof Iran has been involved with attacks in Iraq, adding residents of the beleaguered nation were "victimized by terror and the presence of foreign forces" on their territory.
U.S. State Department spokesman Sean McCormack said the United States will wait and see whether Iran changes its behavior.
Another point of contention between the United States and Iran has been the detention of four Iranian-Americans accused of espionage. McCormack had said the United States would not bring up the issue in the meetings, although U.S. officials have called for the release of the four Americans.
Iraqi Prime Minister Nouri al-Maliki, joined at the talks by Foreign Minister Hoshyar Zebari, appealed for help from the United States and Iran.
"We are hoping that you support stability in Iraq, an Iraq that doesn't interfere in the affairs of others nor wants anyone to meddle in its own affairs," Maliki said in excerpts released by his office, reported the Associated Press.
The U.S.-Iran dialogue marked the second time the two countries have held direct talks in the past few months. The first discussions on May 28 ended a 27-year diplomatic freeze between the nations.
Although Iraq had pressed for a second meeting with the two countries, U.S. officials delayed subsequent talks because Iran had not scaled back its involvement in Iraq.
Following the nearly seven-hour meeting, which was not open to the press, Crocker told reporters that the Iranians said their intention was not to defeat the United States in Iraq. He also said that details on a timetable and participants in a security subcommittee on Iraq would be worked out in coming days.