A 17-year NHL veteran, Numminen received a raise over the $2 million he made last season, when he joined the Sabres as a free agent.
The move is Buffalo's first since free agency started Saturday. The Sabres are trying to bolster their depleted defensive ranks after losing stalwart Jay McKee, who signed with St. Louis. The Sabres lost another free agent Monday when forward Mike Grier agreed to sign with San Jose.
Although the Sabres allowed Numminen to become a free agent, the sides continued talks through the weekend.
Numminen had surgery last week to correct an irregular heartbeat and has been cleared to resume playing. He has since returned to his native Finland, where he spends his summers.
Numminen's agent, Don Baizley, said his client made it his intention to return to play in Buffalo.
Considered Buffalo's steadiest defenseman, Numminen played a big role in helping the Sabres win a franchise-record 52 games and make an extended run in the team's first playoff appearance since 2001. Buffalo reached the Eastern Conference finals before losing Game 7 to eventual Stanley Cup champion Carolina.
Numminen finished second among Buffalo defensemen with 40 points (two goals, 38 assists) in 75 games. That marked his most productive year since a 48-point campaign with Phoenix in 2001-02.
He added a goal and assist and averaged nearly 19 minutes of ice time in 12 postseason games, the first time he's been on a team that advanced past the first round.
The surgery was anticipated after the non-life threatening heart condition forced Numminen to miss one game and part of another during Buffalo's first-round playoff series against Philadelphia.
Numminen returned to the lineup and played in the next eight games before a hip injury sidelined him for five of the team's final six games.
Numminen, who has had a heart murmur since childhood, was diagnosed with a dilated aorta in March 2004 when he was with the Dallas Stars. He missed five games because of the condition before being cleared to play.
Numminen ranks second among European players with 1,235 career regular-season NHL games, 17 short of passing Jari Kurri, a fellow Finn and former Edmonton Oilers great.