The 49ers’ spirited quarterback competition is under way. Of all places, it began at a racquetball court.

That’s where newcomer Josh Johnson encountered 49ers incumbents Alex Smith and Colin Kaepernick, as well as coach Jim Harbaugh, whom Johnson excelled under at the University of San Diego from 2004-06.

“It was guys just getting to know each other and becoming teammates,” Johnson, an Oakland native, said Friday. “The team aspect is more important than anything. We all have to be comfortable with each other.

“Even though everybody wants to play, the team is more important.”

After his racquetball initiation and a visit to the 49ers facility, Johnson signed a two-year deal worth up to $5 million, including a $350,000 signing bonus and a $50,000 roster bonus, a league source confirmed. His base salary is $700,000, and he could earn up to $1.5 million in incentives each of the next two seasons.

Johnson was 0-5 as a Tampa Bay Buccaneers starter, and he was mainly a backup his first four seasons there.

Even though Harbaugh told him Smith is entrenched as the 49ers starter, Johnson jumped at the chance to compete and to do so with similar offensive concepts to his record-setting days at USD.

“Coach has never shot me wrong before. I know it’s all about hard work with him and getting it done on the field,” Johnson said. “He showed me how to play the quarterback position with confidence and to be precise with everything.”

Smith re-signed with the 49ers on a three-year deal but only after the club showed interest in acquiring Peyton Manning.

“I know this is my job,” Smith said Wednesday. “I feel like I’ve earned it. I’ve earned the right to compete for it, and I’ve always welcomed competition and will continue to welcome it.”

Last year, the 49ers traded up to select Kaepernick four picks into the second round, and although Kaepernick saw scarce action as a rookie, the organization is not believed to have soured on him. As much as Harbaugh invoked “the team, the team, the team,” he’s just as fond of competition.

“My college career told me: Look at what I did playing for these coaches, playing in this offense,” Johnson said. “I had tremendous success. We won so many games.

“We accomplished so much as a team and changed so much for San Diego. … Why not do that in the pros as well, to grow up in the pros under the same coaching staff?”

On Wednesday, Johnson visited the Washington Redskins, whose general manager, Bruce Allen, was in the same role with the Buccaneers when Johnson became the first USD product ever drafted (fifth round, 2008).

Johnson was a 5-foot-11, 145-pound teenager when Harbaugh came to Oakland Tech to recruit him, a union spurred by then-McClymonds High coach Alonzo Carter.

While Johnson said he and Harbaugh hit it off immediately with their matching love of football, their reunion will take place on a 49ers team coming off a 14-4 season that ended in the NFC Championship game.

“I know the success will continue, because I’ve played under this coaching staff already,” Johnson said. “I know what they expect out of their players, details that go into the preparation every week. … I’m excited to be part of that again.”

Not even a crowded quarterback corps dampened Johnson’s enthusiasm. Aside from Kaepernick and Smith, the 49ers also have Scott Tolzien, who didn’t play in any games last season as a rookie. Johnson isn’t concerned about how reps will be split in practice.

“I’ve been in worse situations,” said Johnson, who went into the Buccaneers’ 2009 training camp as a fourth-string quarterback and ended up starting four games that season.

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