Woodley made a desperate late comeback to dominate the final round, but Paul clearly deserved the win on the back of being more active and landing more punches.
Paul was officially awarded the victory via a split decision 77-75, 75-77, 78-74.
Woodley said after the fight he believed he had won.
However, it was Paul who was more angry, calling out judge Rogers over his decision to award the fight to his 39-year-old opponent.
"That's bulls***," Paul said.
"It was tougher fight than I expected. My legs felt weird since the locker room. I don't know what's wrong with me.
"This is a dream come true. I want to cry, but I'm a little tired.
"I didn't fight my best tonight. I give myself a C-minus."
Woodley called Paul out in his post-fight interview inside the ring — triggering tempers to boil over as Woodley called Paul a coward for knocking back an opportunity for a re-match.
The result is likely to be Woodley's last fight.
"I felt like I won the fight," he said.
"Jake's a great opponent … I knew he could take a punch. But the fact that one judge gave me two rounds is laughable.
"I want a rematch."