Jackson came in at 211 pounds, five pounds over the light heavyweight limit. The contest will still go on as planned and Jackson will forfeit 20 percent of his fight purse. Bader made weight at 205 pounds.
In a post-fight interview with Fuel TV, Jackson cited an undisclosed injury for missing weight.
The former UFC champion received a warm welcome from the Japanese crowd despite missing weight after having asked UFC brass repeatedly for the opportunity to fight in Saitama. It is the first UFC card in Japan since December 2000.
"I really wanted to fight here," Jackson said. "You guys have no idea. I've had a lot of ups and downs in my camp. Me and (UFC president) Dana White almost bumped heads again but he understood how much I wanted to be here."
Jackson (32-9) is looking to avoid back-to-back losses for the first time in his professional career. He lost via submission to current 205-pound champion Jon Jones in his last fight.
Meanwhile, Bader (13-2) looks to build off a KO win at UFC 139.
All other fighters set to compete at UFC 144 came in on weight. Lightweight champion Frankie Edgar, who looks to defend his belt for the fourth time, came in at 154 pounds. Challenger Ben Henderson weighed the same.
For Edgar (14-1), it will be the first title defense against an opponent he has yet to face. He fought B.J. Penn in an immediate rematch in his first title defense before completing a trilogy against Gray Maynard in his next two fights.
"This is great," Edgar said. "It's been a good camp preparing for him. A new face and a new name. Let's do it."
Henderson (15-2), a former lightweight champion in the WEC, was highly respectful of the champ.
"This is a huge opportunity," Henderson said. "Frankie is the man. He has a great chin and great heart. He's proved himself time and again. It's going to be an honor for me to take the belt from a champion like that."
The UFC 144 pay-per-view card features seven fights instead of the usual five and will last four hours.
Several notable Japanese stars look to secure wins for the home crowd. Lightweights Takanori Gomi and Norifumi Yamamoto each look for important wins to turn around disappointing runs in the UFC so far.
Brett Okamoto covers mixed martial arts for ESPN.com. Follow him on Twitter.