The 34-year-old Brazilian, who also holds the featherweight title, becomes the first two-time double champion in UFC history.
Pena shocked the world when she submitted her opponent in the second round of their title fight back in December. The fight went on to claim the 2021 UFC Upset of the Year award, as well as a host of other outside accolades.
Nunes, adopting a southpaw stance that she has rarely shown in previous fights, stunned Pena with two right handers in the first round. She then floored her American opponent three times in the second to become the first woman in UFC history to knock an opponent down three times in the same round.
The Brazilian took Pena to the floor again several times over the final few rounds and hit her with more slashing elbows. She did have to survive a threatening attempt at an armbar submission midway through the fourth round as Pena fought back.
Judges awarded Nunes the victory by unanimous decision - 50-45, 50-44, 50-43.
"We make history again, this is the best day in my life," said Nunes after the fight.
"The best thing I did was make my dream happen.
"I feel like I can grow even more now - I've evolved even more.
"Now I have a chance to go back to Brazil and see my family that I miss so much. Please let me rest a little, and I'll come back as soon as possible."
UFC chief Dana White confirmed Pena was taken to see specialists after the fight.
White said: 'Julianna's got a big chunk missing from her forehead.
'She's going to see a plastic surgeon right now.
'She got pretty banged up tonight, she got five or six knockdowns in the first two rounds.
'She was hurt. She needs to take some time off, relax, spend some time with her daughter and then we will go from there.'