James is now enjoying the best of both worlds, getting on the field after a season-ending Achilles tendon injury to Kendall Hunter and even running option plays with quarterback Colin Kaepernick similar to the ones that piled up all that yardage at Oregon.
James scored on a 15-yard run with the 49ers trailing the Atlanta Falcons 17-0 in the NFC Championship game, sweeping to his right as an offset back out of a spread formation.
"It was like an Oregon play, and Colin made a great read," James said this week.
James is back in the big game spotlight and will spell starter Frank Gore as well as return kickoffs in Super Bowl XLVII in the Superdome.
Watching from street clothes for the first 12 games of his NFL career after servicing the first-team defense for the scout team isn't what James had in mind after being drafted by the 49ers.
"I can't sit here and say it was fun," James said. "Anytime you're a competitor, you want to be on the field, helping your team win, so I had to do it throughout practice. It didn't give an excuse to slack off and not try to get better because you never know when your number is going to be called."
The 49ers, in contrast to Oregon, operate at a deliberate pace sometimes even drawing criticism for using too much of the play clock and not getting to the line of scrimmage quickly enough.
Play-calling had more verbiage and was much more involved. It was evident early on that James was a Duck out of water.
"I can still remember the first minicamp when he showed up coming from Oregon's offense and what a difference it was," offensive coordinator Greg Roman said. "We're a team that huddles. [Oregon] might say one word and that means a play and they don't have a lot of plays. We literally have hundreds of plays."
Recalled James: "I hadn't been in a huddle since high school. After being in a huddle and then having to remember [the play] and not just run it it was a little bit different for me."
James did his best to learn the 49ers offense while running the plays of the opposing team each week. He also worked on other parts of his game while coach Jim Harbaugh watched closely.
"His work ethic was really evident," Harbaugh said. "He was taking as many reps as he possibly could on the scout team. He would do it as a running back, he would do it as a receiver. And he really improved his hands a great deal."
Two things happened to hasten James' development. First, Hunter suffered an Achilles tear Nov. 25 against New Orleans and was placed on injured reserve.
Second, Kaepernick had become the full-time quarterback, bringing with him the kind of read-option football James had played at Oregon.
"Colin's game adds a different dimension to the offense, and it's something I'm familiar with, running the spread," James said.
James carried 27 times for 125 yards in the last four regular-season games, but his biggest play came on special teams, a 62-yard kickoff return against New England after the Patriots had rallied from a 31-3 deficit to tie the score 31-31 midway through the fourth quarter.
It set up a 38-yard Kaepernick-to-Michael Crabtree touchdown pass on the next play, and the 49ers won 41-34.
"Once he started getting comfortable, we saw a dynamic football player," 49ers safety Donte Whitner said. "Coming from a big university, playing in big games and being a big-time player, having to sit out and be humbled like that, it's a testament to the character he has."