Team owner Paul Allen confirmed Wagner's extension on his Twitter account Saturday night. The deal is worth $43 million, a source confirmed to ESPN, making him the highest-paid middle linebacker in football.
"I'm thankful for it. If I would have waited any longer I probably wouldn't have been as patient," Wagner said. "But you know it's a crazy process and I'm glad it's over."
Signing Wagner and quarterback Russell Wilson, both of whom are entering their fourth season in the league, to extensions were top priorities for the Seahawks this offseason.
Wagner's deal became a challenge after the team signed Wilson to a new contract worth $87.6 million. That deal included a signing bonus of $31 million, according to Wilson's agent, Mark Rodgers, bringing Wilson's cap number over $8 million.
The Seahawks were hoping to get a cap number around $5 million for Wilson and $3.5 million for Wagner.
"It's kind of fit into our expectations. We've seen it happen. I kind of trust the way we've laid it out that [general manager] John [Schneider] is going to be able to get it together and pull it off and we just have. We've done every single thing we've tried to do along the way," Seattle coach Pete Carroll said.
"I'm not surprised by it. I'm surprised there are so many questions. We have continued to do our work. We have a real approach, really no surprises if you've watched us now, which is a good thing. It means you have a philosophy and have a manner by which you can discipline yourself and do the work you say."
After Wilson signed, Wagner said he considered holding out but decided to show up for the start of Seahawks training camp and avoid paying a fine.
Wagner was an All-Pro last season and has been the Seahawks' starting middle linebacker since being a second-round pick in 2012.
Asked whether it was important to be the highest-paid linebacker, Wagner said, "It's important to be recognized as one of the best."
"It's definitely a weight off your shoulders off the field because off the field you think about it a lot and you wonder if you're going to be here or not going to be here but like I said I'm thankful to them for letting me be a part of this for four more years," Wagner said.
With Wagner's extension signed, most of Seattle's top defensive players now are under contract for at least the next three years, including cornerback Richard Sherman and safeties Kam Chancellor and Earl Thomas. Chancellor, however, is currently in the midst of his own holdout.
"Our focus is never off of Kam. He is such an integral part of this team and the guys love him so much," Carroll said. "Since we've needed to turn our attention to it we have been but now we really can get after it. I'm hoping we can get him back here as soon as possible."
Information from ESPN's Adam Schefter and John Clayton and The Associated Press was used in this report.