Samardzija, who is not arbitration eligible, will remain with the team for at least four more years unless he's released or traded.
Under the terms of the collective bargaining agreement, Samardzija's salary can not be cut more than 20 percent from his 2011 salary.
The former Notre Dame All-American receiver signed a five-year, $10,250,000 deal after being drafted by the Cubs in the fifth round in 2006.
Samardzija made $2.8 million in 2011, and with a 20 percent cut, he'll make $2,640,000 in 2012, including a $400,000 pro-rated signing bonus from a contract he signed in 2006.
"Hey, I know my contract was from the last regime, but this is a business," Samardzija said. "They did what they had to do. I'm fine with that.
"I'm looking forward to playing for Theo Epstein and Jed Hoyer. They may be young guys, but they're young and accomplished guys. They have two world championships under their belt, and that's good enough for me."
Samardzija gave credit to former general manager Jim Hendry, who was fired in July, for signing him and playing baseball over football.
"I'll miss Jim, he's one of a kind, and he was a major reason why I chose to play baseball over football," Samardzija said. "But it's a new day with the Cubs. I'm just hoping they have a plan for me and I'm hoping that plan is as a starting pitcher."
Samardzija will begin throwing in Mesa, Ariz., right after Thanksgiving.
The 26-year-old pitcher had his best season in 2011, compiling an 8-4 record with a 2.97 ERA. He also was second on the team to Sean Marshall in appearances with 75.
The eight wins were the most by a Cubs reliever in 25 years, since Lee Smith in 1986.
Bruce Levine covers baseball for ESPNChicago.com and ESPN 1000.