The Crimson Tide (12-1) finished No. 2 with a 0.944 ranking after its suspenseful 32-28 victory over former No. 3 Georgia Saturday in the SEC title game.
The Fighting Irish (12-0), who were idle this week, retained the No. 1 ranking with a near-perfect 0.998 mark.
Notre Dame and Alabama will square off at Miami's Sun Life Stadium on Jan. 7 for the college football championship. The defending champion Tide have won the crown in two of the past three seasons.
Georgia, meanwhile, fell from third to seventh and Florida took its place, guaranteeing the Gators an at-large BCS berth.
Oregon, Kansas State, Stanford, Louisiana State, Texas A&M and South Carolina rounded out the Top 10.
The other BCS bowl pairings finalized Sunday include No. 12 Florida State vs. Northern Illinois in the Jan. 1 Orange Bowl; sixth-ranked Stanford vs. Wisconsin in the Jan. 1 Rose Bowl; Florida against No. 21 Louisville in the Jan. 2 Sugar Bowl; and No. 4 Oregon playing fifth-ranked Kansas State in the Jan. 3 Fiesta Bowl.