He was attracted by the punishing defense, the strong running game and a coaching staff he trusted.
The 49ers announced Thursday that Manningham had signed a two-year deal to join the team he helped knock out in the NFC championship game two months ago in their latest offensive upgrade at wide receiver. The team also announced Thursday it re-signed Ted Ginn Jr. to a one-year deal.
San Francisco also agreed to a two-year deal with quarterback Josh Johnson, a league source told ESPN's Josina Anderson. Johnson, a fifth-round pick in 2008, spent his first four seasons as a reserve with Tampa Bay. Johnson played for 49ers coach Jim Harbaugh in college at San Diego.
Manningham agreed to the deal last Saturday when the 49ers were in the thick of the race to sign Manning, the four-time NFL MVP and brother of his old quarterback with the New York Giants, two-time Super Bowl winner Eli Manning.
Peyton Manning ended up choosing to sign with Denver and the Niners brought back Smith.
"I wanted to go there and I knew that Peyton Manning was going to go somewhere. I thought he was coming to the 49ers but he didn't," Manningham said. "He went to Denver. Good luck to him with that. I wish the best for him. We got Alex Smith and I know he's a great player.
"I knew (playing with Manning) was a possibility but I wasn't picking them because of that. I know Peyton Manning is a great quarterback and everything but if you don't have a good defense ... offense can be potent but there's really no point."
The 49ers defense was one of the best last season and played a big part in the team's 13-3 record and trip to the NFC title game that ended with a 20-17 overtime loss to Manningham and the Giants.
San Francisco has now made moves to improve the offense, especially at wide receiver, where Manningham and fellow newcomer Randy Moss will join Michael Crabtree in a unit that should help Smith develop even more as a potent passer. Crabtree was the only 49ers wideout to catch more than 20 passes last season.
"I feel like I can come there and make an impact and be a great addition to this offense," Manningham said.
Manningham has 160 catches for 2,315 yards and 18 touchdowns in his four-year career after being drafted out of Michigan in the third round in 2008. He was limited to 12 games last year because of injuries and had only 39 catches for 523 yards and four scores in his least productive season since his rookie year.
"We are very pleased to add a player like Mario to our team," general manager Trent Baalke said. "Although it is still early in his NFL career, he is a productive wide receiver with a lot of big-game experience. He will be a nice complement to our current wide receiver group and a good fit for our offensive system."
Manningham took off in the postseason, catching TD passes in wins over Atlanta and Green Bay to get New York to the NFC title game. He then had a go-ahead 17-yard touchdown catch in the fourth quarter of the Giants' overtime win over San Francisco to get to the Super Bowl and capped the postseason with a memorable catch.
His over-the-shoulder 38-yard catch between two defenders, on which he managed to stay inbounds and hold onto the ball despite being hit, started the game-winning, 88-yard touchdown drive for the Giants.
But despite that, New York showed little interest in keeping Manningham, who ultimately picked San Francisco over St. Louis.
"That's the business part about this system, about football. I would have wanted to come back to the team that I started with. I won a Super Bowl with those guys," he said. "This is my new team now."
Having played the Niners in both the regular season and playoffs this past season, Manningham knows how good San Francisco is on defense.
The 49ers led the league in run defense and forced turnovers and were second in scoring defense. That entire starting unit is expected back in 2012 with cornerback Carlos Rogers and linebacker Ahmad Brooks re-signing and safety Dashon Goldson getting the franchise tag.
"They swarm, they'll hit you and they'll cover you," Manningham said. "I feel like they have the best linebacking corps in the league. They have athletic defensive backs, D-line, they're all really good. It's a great defense out there."
Information from The Associated Press was used in this report.