First-half goals by Norwegian striker Mohammed Abdellaoue and defender Christian Schulz put Mirko Slomka's Hannover in control before Ivory Coast striker Didier Ya Konan added a third in the 89th minute.
The victory allows Hannover to leap-frog both Leverkusen and Mainz into second.
Third-placed Mainz lost at Stuttgart on Saturday and defending champions Bayern Munich were held to a 1-1 draw at Wolfsburg leaving Dortmund in control of the Bundesliga and heading towards their first league title since 2002.
Dortmund blitzed Leverkusen 3-1 on Friday with three goals in six minutes as Jürgen Klopp's young side showed no sign of releasing their grip at the top.
Goals by Mario Götze and Kevin Grosskreutz sealed the win, but Michael Ballack spent the game on the bench as the Germany captain looks to return from a leg injury.
Less than 24 hours later, Wolfsburg held Bayern at home despite their ex-England coach Steve McClaren selling striker Edin Dzeko to Manchester City over the German league's winter break.
Wolfsburg lacked firepower up front against Bayern, but showed dogged domination against the champions to force an equaliser through defender Sascha after Thomas Müller had given Bayern an early lead.
Both sides missed penalties in the first-half and Bayern goalkeeper Thomas Kraft, making his Bundesliga debut, pulled off a stunning reflex save to deny Brazilian striker Grafite's spot-kick to leave Munich fifth in the league.
Bayern's Dutch star Arjen Robben conceded Dortmund may now be too far ahead for Munich, who are 16 points off the pace, to retain their title.
"There's no point talking about first place any more, as several of us have already said," admitted Robben after making his first appearance of the season.
Despite limping off with a knee injury after just 25 minutes, Bayern's midfield star Franck Ribery is only expected to miss five days after a scan on Sunday revealed his knee injury is not as bad as first thought.
In Saturday's late match, Real Madrid target Ruud van Nistelrooy scored the only goal in Hamburg's 1-0 win over Schalke, who have reached the last 16 of the Champions League, and admitted he is tempted to return to Spain.
Real are reported to be interested in re-signing the Dutch striker, who spent four years in Madrid, but the German side want to hold onto their forward.
The result leaves Schalke 10th and Hamburg seventh.
Bottom side Borussia Mönchengladbach gave themselves a boost in their battle to stay up with a 1-0 win at Nuremberg with goalkeeper Christofer Heimeroth making a dramatic late penalty save.
Senegal striker Papiss Demba Cisse scored twice to go top of the league's goalscoring list with 15 goals as he helped Freiburg sneak a 2-2 draw at St Pauli which keeps them sixth.
Bremen picked up a rare win after captain Torsten Frings drilled in a free-kick in the second minute of injury time to seal a 2-1 win over Hoffenheim which left his side 12th.