Harbaugh turned Smith into a steady winner at last, a playmaker and playoff star.
Smith still looks to be San Francisco's man behind center, even after his coach and team flirted with Peyton Manning.
Smith had been weighing a three-year offer from the Niners early last week when Harbaugh and offensive coordinator Greg Roman traveled to Duke to work out Manning. For Smith, there might be some hard feelings - but maybe not.
This guy has seen it all during his seven-year NFL career after the 49ers selected him with the No. 1 overall pick out of Utah in 2005.
If Smith is offended by his coach's brief courting of Manning, perhaps a heart-to-heart sit-down could mend any hurt feelings. After all, Harbaugh has long declared his admiration for Smith, who caddied for his coach during last month's Pebble Beach National Pro-Am.
49ers CEO Jed York told CSNBayArea.com on Monday that Smith's offer was still available and, "We'd like for him to be here, and we'll see where it goes."
"Obviously I always wish him the best, whatever he decides is best for his career and his family," San Francisco kicker David Akers said by phone Monday. "I think he's a great guy and a great player, obviously he showed us what we needed as a team leader this year. I'd love to continue to play with him. I'd love to play with a lot of guys I don't get to. That's part of the business. You just have to get used to that."
While the 27-year-old Smith flew to Miami on Sunday, few had envisioned the free agent QB signing all the way across the country. He has long made it clear he would like to stay put with San Francisco, and that could be even more true now that the Niners added talented wideouts Randy Moss and Mario Manningham last week to open up the field.
Will Smith be the one throwing them the ball? That should all be settled soon now that Manning has made his choice. Manning and Smith both are represented by agent Tom Condon of CAA Sports.
Smith has always said the right thing - he even started to sound like Harbaugh himself last season after working closely with the former 15-year NFL quarterback - when it comes to the business side of football, so he might not blame Harbaugh and general manager Trent Baalke for at least exploring the idea of adding a player with the pedigree of four-time NFL MVP Manning.
The 49ers were the only team among the three believed finalists in the Manning chase that didn't publicly acknowledge their interest, and it is believed their offer to Smith still stands. But who knows whether they will give him a slight bump to the reported $24 million contract after what Smith endured playing the waiting game during the recent days.
Smith, who made $4.9 million in base salary last season and then earned a $1 million bonus for reaching the playoffs, thrived under Harbaugh and helped lead the franchise to its first postseason berth and winning record in nine years.
What a turnaround for the guy who had been relentlessly booed by his home fans at Candlestick Park in previous years. Harbaugh gave him a clean slate last season and the reins to the offense.
Smith gets the highs and lows in this league, always has.
He took over as 49ers starter midway through 2009 and was entrenched as the No. 1 heading into 2010. After separating his non-throwing left shoulder that Oct. 24 at Carolina, former coach Mike Singletary turned to 2006 Heisman Trophy winner Troy Smith for the next five games - even after Alex Smith was healthy again. Troy Smith went 3-2 as a starter, then it was Alex Smith's turn again for two games, including a commanding win over eventual '10 West champion Seattle.
After a flop at San Diego, Singletary turned back to Troy Smith for a must-win game with the Rams on Dec. 26. That 25-17 loss cost the coach his job with one week to go. Jim Tomsula, serving a single-game stint as interim head coach, went with Alex Smith for a win against Arizona in the season finale.
One thing Smith insists he has learned along the way is to remain even-keeled and to control what he can control. He has said his tool last year was staying within himself and not forcing things as he did in the past.
Smith threw for 3,150 yards and 17 touchdowns with only five interceptions as San Francisco went 13-3 to win its first division title since 2002.
San Francisco went 6-2 on the road and won four of those games in comeback fashion - and Smith rallied his team from behind five times in all, not to mention a 36-32 victory against the favored Saints in the NFC divisional playoffs. Smith completed a 14-yard touchdown pass to Vernon Davis with 9 seconds left to seal it after Drew Brees had put his team ahead.
The Niners had 38 takeaways to only 10 turnovers in 2011 for a plus-28 turnover differential. That matched the second-best mark in NFL history since 1941.
Smith's heads-up decision-making was a big reason for that.
"I hope he can stay, but I understand the business," Akers said. "I was fortunate to play with one team for so many years."
AP Sports Writer Steven Wine in Miami contributed to this story.