John Alder and Liam Sweeney were aboard the Malaysian Airlines flight from Amsterdam to Kuala Lumpur when it crashed in Eastern Ukraine on Thursday afternoon.
Mr Alder, who was known to many Magpies supporters as "the Undertaker" because of his distinctive matchday dress, had barely missed a game home and away in almost 50 years following the club.
Manager Alan Pardew, who was due to fly out to New Zealand with the squad on Friday afternoon, said: "Myself and all the players are deeply shocked and saddened by this terrible news.
"We all knew how passionately John and Liam supported the team and the club.
"They were with us just earlier this week for our first pre-season friendly against Oldham and their dedication to travel all the way around the world to support us in New Zealand tells you all you need to know about the passion they had for Newcastle United.
"Our hearts go out to their families and friends."
The club is to dedicate an area around the Sir Bobby Robson statue at St James' Park for fans to lay their tributes, and the manager and players will wear black armbands for the games against Sydney FC and Wellington Phoenix.
In addition, the lives of the two men will be marked at the first Barclays Premier League game of the season against Manchester City.
Managing director Lee Charnley said: "The loss of John and Liam is truly devastating news. Both men were dedicated supporters of our Club and were known to thousands of fans and staff alike.
"On behalf of everyone at Newcastle United, we send our deepest condolences to John and Liam's families and friends.
"The club will be dedicating an area surrounding the Sir Bobby Robson statue for fans to pay their respects to John and Liam.
"The manager and players will also be wearing black armbands for both their games against Sydney FC and Wellington Phoenix in the Football United Tour of New Zealand.
"Arrangements will be made to pay tribute to the two men at the club's first Premier League game against Manchester City on Sunday, August 17. Further information regarding this will be announced in due course."
Magpies goalkeeper Tim Krul has also paid his respects to the two men on Twitter.
He said: "2 Geordies on plane MH17 travelling to watch Nufc in New Zealand. RIP John Adler and Liam Sweeney.. Our thoughts are with all the families."