The 49ers had been working to re-sign Smith, the No. 1 overall 2005 draft pick who 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.
The Dolphins' unexpected courtship of Smith came after they were spurned by Manning and then hosted former Green Bay Packers backup quarterback Matt Flynn for a weekend Saturday.
It was unclear whether the Dolphins expanded their quarterback search in a bid to pressure Flynn to sign soon. He visited the Seattle Seahawks earlier in the week.
Flynn left South Florida on Sunday morning, but a deal with the Dolphins remained a possibility, said his father, Alvin.
A second person told the AP the Dolphins were to host quarterback David Garrard on Monday.
Garrard, a starter for Jacksonville from 2005 to 2010, didn't play last year. He was released five days before last year's opener by the Jaguars, then underwent back surgery in October.
But it was Smith's turn on Sunday
He landed at the Fort Lauderdale airport Sunday morning and arrived at the Dolphins complex at 11 a.m. EDT in a car driven by trainer Kevin O'Neill. New coach Joe Philbin, new offensive coordinator Mike Sherman and general manager Jeff Ireland arrived earlier.
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.
All were also on hand for Flynn's 5 1/2-hour meeting Saturday.
Flynn was a backup the past four years for Green Bay, where his offensive coordinator was Joe Philbin, the Dolphins' new head coach. Flynn has only two career NFL starts, but in last year's regular-season finale he set franchise records with 480 yards passing and six touchdowns to help the Packers beat Detroit 45-41.
The Dolphins have started 16 quarterbacks since Dan Marino retired and are looking to make another change. While incumbent Matt Moore played well last year, there are doubts he's a franchise quarterback. 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 Tuesday for Harbaugh at Duke. The four-time NFL MVP also worked out for the Broncos on Friday at Duke, and for the Titans on Saturday in Knoxville, Tenn.
Manning has been rehabbing in North Carolina following a string of neck surgeries, which led Indianapolis to release him.
San Francisco running back Frank Gore, who works out each offseason in Miami, said Sunday he hadn't spoken to Smith. Gore has long supported Smith through the quarterback's up-and-down seven NFL seasons.
Now, Gore and the 49ers are sitting tight to see what happens next.
"It's crazy," Gore said. "I'm waiting for whatever happens. I know coach Harbaugh and (general manager) Trent Baalke feel good about what they're doing."
Manning's whirlwind free agency tour officially kicked off soon after he bid farewell to the Colts in an emotional press conference.