The contract contains club options covering 2013 and 2014.
Minaya became general manager in 2004 and was signed to a five-year deal. The Mets made it to Game 7 of the National League Championship Series in 2006. The next two years they missed out on the playoffs on the last day of the regular season.
"We failed this year, and we want to get the redemption that we need and move forward," Mets chief operating officer Jeff Wilpon said. "We obviously were not a very good team when Omar came aboard, and he's turned this thing around, and we think he deserves another chance to keep getting us to where we want to be."
The Mets also are trying to negotiate a new contract for Jerry Manuel , who became interim manager in June when Willie Randolph was fired.
RED SOX: Boston pitcher Josh Beckett threw a side session of 67 pitches Thursday during an off-day in the Red Sox-Angels playoff series, and remains scheduled to start Game 3 Sunday in Boston.
Beckett, originally scheduled to start Game 1, injured a muscle in his side last Friday during a bullpen session.
DEVIL RAYS: Tampa Bay closer Troy Percival was left off the roster for the American League division series against the Chicago White Sox because of back tightness. Percival had 28 saves this season, but just one came after Aug. 13.
Dan Wheeler filled in for Percival, and converted 13 of 18 save opportunities. He earned another save in Thursday's 6-4 win over the White Sox.
ROCKIES: First baseman Todd Helton had surgery on his lower back and is expected to be ready for spring training.
Helton, a career .328 hitter, batted just .264 with seven homers and 29 RBI in 83 games this season.
ASTROS: Relief pitchers Geoff Geary and Chris Sampson both had successful surgeries.