The 31-year-old, who finished the fight with his white shorts stained pink, sustained a large gash above his eyebrow and a smaller one in his eyelid in the third round and a constant trickle of blood troubled him for the remainder of the bout.
It was also a concern for referee Tony Week who, on several occasions, asked the Mancunian's corner to tend to the cut and called in the doctor towards the end of the sixth round with genuine concerns the fight could be stopped.
However, Fury battled through and – as his opponent tired – he began to take control, despite still being hampered by the injury.
This was intended as a stop-gap fight ahead of an expected rematch with Deontay Wilder in February but if Fury was hoping to make a statement this was not it.
With the eye causing him a problem and no idea how long he would be allowed to continue, he tried to step up the attack after the doctor's inspection and landed two big right-handers in the seventh round, one which rocked Wallin back onto the ropes, and a few more punches found their target in the eighth and ninth.
Although the Swede, unbeaten in his first 20 fights but stepping up a level here, looked to be tiring he managed to grind it out to the final round where, sensing his one final opportunity, landed a big left early and Fury was more than happy to cling onto his opponent in an attempt to avoid further trouble.
But despite Wallin thinking he had done enough the win was a unanimous one for Fury, 116-112, 117-111, 118-110.
Fury said: "I know Otto's father (who died earlier this year) would be very proud of his son.
"It was a great fight, I got caught on the eye and that changed the fight. For the majority I could not see out of the eye. Then there was a clash of heads and I got cut again.
"I hit him with some good shots, some big body shots.
"A good 12 rounds, he was tough. Deontay Wilder, I want you next, bum. That's my fourth fight, it has put me in good stead for the big dosser, February 22nd. Let the cut heal, have some time to relax with the family.
"I haven't seen the cut, it feels quite bad, but I'm the Gypsy Warrior. It's all heart and determination. If I can keep going, I will keep going. He was 20-0 didn't know how to lose but he does now."