The next week, with both No. 1 Ohio State and No. 2 Michigan's regular season complete, No. 3 USC defeated then No. 5 Notre Dame. Fourth-ranked Florida defeated unranked in-state rival Florida State. With the victory over Notre Dame, USC passed Michigan in the polls, taking over the BCS No. 2 spot. Michigan fell to No. 3 with Florida remaining No. 4 and Notre Dame falling to No. 10.
The last week of the regular season was dynamic for the national championship race. Third-ranked Michigan remained idle. Fourth-ranked Florida faced No. 9 Arkansas in the SEC Championship, while No. 2 USC faced unranked, in-city rivalUCLA. Both Florida and Michigan cheered as USC fell to UCLA 13–9. Florida defeated Arkansas to claim the 2006 SEC Championship Title. USC's loss knocked them out of contention, leaving No. 3 Michigan and No. 4 Florida as the most likely teams to earn the No. 2 ranking and face Ohio State for the BCS National Championship. The final BCS poll passed Florida over Michigan to take the No. 2 spot while Michigan remained unchanged at No. 3, with .0101 points separating the two teams. This small difference was a result of the human polls (the Coaches Poll and Harris Interactive Poll) ranking Florida above Michigan while the computer polls had the two teams tied for second.
There were many theories how Florida jumped Michigan in the final poll. Some sportswriters theorized that it was not a matter of which was the better team, claiming Florida had an advantage in the polls because they had played the last two weeks while Michigan had not, or that voters were swayed due to Florida coach Urban Meyer's "campaign" to get Florida into the BCS National Championship Game. The fact that the difference in the final BCS Poll was due to human voters, not computer rankings, gives some credence to these theories. Other theories suggest that since Michigan did not win their conference title, they did not deserve to play for the BCS National Championship, or that a rematch between Michigan and Ohio State was not favored by the poll voters. The controversy was largely resolved when USC defeated Michigan 32–18 in the 2007 Rose Bowl, and Florida beat top-ranked Ohio State 41–14 in the BCS Championship Game.
The Buckeyes got off to a fast start when receiver Ted Ginn Jr. returned the opening kickoff 93 yards for a touchdown, giving Ohio State a 7–0 lead only 16 seconds into the game. During the celebration following the return, Ginn was injured and would miss the remainder of the game. The Gators quickly rebounded, however, leading a quick 46-yard drive for a score, capped off by a 14-yard touchdown pass from Chris Leak to Dallas Baker. After stuffing the Ohio State offense to a quick punt, Florida drove 36 yards for a touchdown on a 4-yard run by Percy Harvin. On their next possession, the Gators once again drove in for a score, going 71 yards on 10 plays and getting it in the end zone on a 2-yard run by DeShawn Wynn on the first play of the second quarter.
Ohio State came back for a score of their own with an 18-yard touchdown run by Antonio Pittman to bring the score to 21–14. After a Florida field goal, Ohio State coach Jim Tressel took a gamble by going for a fourth-and-one from the Buckeyes' own 29-yard line. The Gator defensive line stopped Chris Wells in his tracks and the ball was turned over on downs. Chris Hetland, Florida's much-maligned kicker who was only 4-of-13 for the year, hit his second field goal of the night, making the score 27–14, and with just over two minutes left to play in the half, it appeared that would be the score heading to the break. As Ohio State started from their own 20, quarterback Troy Smith dropped back to pass and was hit by Florida lineman Jarvis Moss, jarring the ball loose. Florida recovered on the Buckeye 5-yard line and punched it in with a one yard touchdown pass from quarterback Tim Tebow to Andre Caldwell. The half ended and the teams went off the field with Florida leading 34–14.
The second half saw a much more defensive game, with no scoring in the third quarter. The Gator offense used up the clock, while the defense continued to stifle Ohio State's purportedly explosive attack. The lone score of the half came with just over 10 minutes left in the game, when Tim Tebow ran in a one yard touchdown score, bringing the tally to 41–14, which was the final score.
Chris Leak was named the offensive player of the game, and Derrick Harvey earned the defensive honors. The Gators held the Buckeye offense to only 82 total yards for the game, and Heisman Trophy winner Troy Smith completed only four passes for 35 yards and an interception. The Gators also dominated in time of possession, limiting the Ohio State offense to just over 19 minutes.
Florida later defeated Ohio State 84–75 in the 2007 NCAA Men's Division I Basketball Tournament on April 2, 2007, marking both the first time in NCAA history that the same two schools have played for the football and basketball championships in the same year and the first time that a school has held both the football and basketball championships in the same academic and calendar year.