Smith left the Miami complex after a 5 1/2-hour meeting. Dolphins officials declined to comment on any details about this visit.
The 49ers had been working to re-sign Smith but also went to North Carolina last Tuesday to watch Manning work out at Duke. Smith, the No. 1 overall 2005 draft pick, enjoyed his best season in 2011 under first-year 49ers coach Harbaugh, a former NFL quarterback.
Smith and Manning have the same agent, Tom Condon.
A new starting quarterback would be the Dolphins' 17th since Dan Marino retired following the 1999 season. Winless in postseason since 2000, they made signing Manning their top offseason priority, but he told them Thursday he would sign elsewhere.
They then courted Flynn, the former Green Bay Packers backup who had ties to new Dolphins coach Joe Philbin. Flynn visited Miami on Saturday, then agreed to terms Sunday on a multiyear deal with the Seattle Seahawks.
The Dolphins planned another QB interview Monday, when they were to host veteran David Garrard, a person familiar with the negotiations said. The person confirmed the visit to The Associated Press on condition of anonymity because the team had not publicly discussed its plans.
Garrard, a starter for Jacksonville from 2005 to 2010, didn't play last season. He was released five days before the opener by the Jaguars, then underwent back surgery in October.
After all of their shopping, it's possible the Dolphins will stick with incumbent Matt Moore.
"Looks like Miami (is) going with Moore again," former Dolphins coach Jimmy Johnson tweeted after Flynn's deal with Seattle was announced.
While Moore played well last year, there are doubts he's a franchise quarterback.
Smith struggled early in his career but threw for 3,150 yards and 17 touchdowns with only five interceptions last season as San Francisco went 13-3 and made the NFC title game after an eight-year playoff drought. He orchestrated six comeback wins, four on the road.
Smith has been weighing a three-year offer from the 49ers. If he instead joins the Dolphins, he would be reunited with running back Reggie Bush. They were teammates at Helix Charter High School in La Mesa, Calif.
He landed at the Fort Lauderdale airport Sunday morning and arrived at the Dolphins complex in a car driven by trainer Kevin O'Neill. Philbin, new offensive coordinator Mike Sherman and general manager Jeff Ireland arrived earlier.
Chad Henne, who started 31 games for Miami over the past three seasons, signed Wednesday with the Jacksonville Jaguars as a backup.
The 49ers emerged as a contender for Manning when the news surfaced that he worked out for Harbaugh at Duke. Manning also worked out for the Broncos on Friday at Duke, and for the Titans on Saturday in Knoxville, Tenn.