Wagner, who has previously had county stints with Lancashire and Essex, will join ahead of the start of Yorkshire's Division Two opener against Leicestershire on April 6. His deal runs until the end of July, when there will be a lengthy break in the Championship for the Hundred and One-Day Cup.
"We are delighted to have confirmed the signing of Neil for the opening ten rounds of the Championship," Yorkshire's managing director of cricket, Darren Gough, said.
"His record in first-class cricket is phenomenal, and the impact he has had on Test cricket playing for New Zealand has been huge. We are blessed to have some great bowlers to choose from within our ranks and believe that, with the addition of Neil, we have the bowlers to bowl any team out".
Wagner, 36, is New Zealand's fifth-highest Test wicket-taker with 246 at 26.71. He has taken almost 800 wickets in his first-class career, and also has a Championship winner's medal from the 2017 season with Essex.
Wagner said: "I've always enjoyed playing my cricket in England and to be getting this opportunity again at such a big club like Yorkshire CCC is a great honour. I feel like I can offer a lot to the team with my experience, attitude and skill set, so I can't wait to get going. I want to be a big part of helping move the team back up into Division One."
Shan Masood, the Pakistan batter, will take on the captaincy next summer, while fast bowler Matt Milnes and allrounder Ben Mike have been recruited from Kent and Leicestershire respectively.