San Francisco general manager Trent Baalke confirmed the meeting Thursday night, but would not disclose when it occurred. The 49ers arrived in Baltimore on Tuesday night for Thursday's preseason game with the Ravens.
Smith did not play Thursday night, but warmed up and was in uniform.
A decision on potential discipline likely will come this month as the 49ers prepare for the regular season. Goodell has routinely met with troubled players at the league offices before making disciplinary decisions.
Smith was sentenced to 11 days of work release last week in a Santa Clara County (Calif.) court after his September 2013 arrest for drunken driving. It was his second such arrest since entering the NFL in 2011. Also, Smith had three felony gun charges knocked down to misdemeanors last week.
Smith voluntary missed five games last season when he entered a substance-abuse treatment center. In October, in London, Goodell told reporters Smith's aggressive approach to his problem could be considered when potential discipline was addressed.
In April, Smith was arrested on an alleged fake bomb threat, but the Los Angeles City Attorney's office declined to press charges. Smith is set to meet with officials in Los Angles to discuss and close the matter July 30.
Smith, the No. 7 overall draft pick in 2011, has 42 sacks in 43 regular-season games.