The judges scored the fight 50-45, 49-46 and 50-45. ESPN.com had Cruz winning 50-45.
It was the fourth title defense for Cruz, the most by any 135-pound fighter under the Zuffa banner.
"It was a tough fight; the kid set a tough pace," Cruz said. "He didn't surprise me. I knew I had to use my strength to slow him down."
Cruz (19-1) used his superior size, strength and striking to keep the much smaller Johnson struggling to get into any kind of offensive rhythm.
Every time Johnson came forward to attack, Cruz caught him with an uppercut left or straight right. Cruz also used his leverage to take Johnson to the ground easily.
Though only one judge found a round to give to Johnson, the challenger could leave the Octagon with his head held high.
At no time in the fight did Johnson stop pressing the action. He set such a torrid pace that Cruz was breathing heavily by the second round.
But the punishing strikes from Cruz took their toll on Johnson (9-2). By the start of the final round, Johnson's left cheek was swollen.
"He was very strong, a lot stronger than I thought he was," Johnson said. "I was surprised by how strong he was. He's a good champion."
Struve forces Barry to tap in second
Struve applied a triangle choke and forced Barry to tap at the 3:22 mark.
"I've been working hard on my kickboxing and showed it in the first round," said the 6-foot-11 Struve, who is a foot taller than Barry. "I'm happy with the result in the first round."
Both Struve and Barry entered this fight having lost their previous fights by knockouts.
Struve improved to 22-2; Barry dropped to 6-4.
Johnson stops Brenneman in first
He made certain Brenneman never got a chance to use that part of his game. Johnson used his superior size, strength and striking to register a first-round TKO.
A left head kick at the 2:49 mark dropped Brenneman, forcing referee Mario Yamasaki to jump in immediately and prevent further damage.
"Everybody was talking bad about my last performance against Dan Hardy, so I had to come out here and do something," Johnson said after improving to 10-3. "Charlie is the first guy who had me nervous before a fight because of his tremendous wrestling."
Brenneman, who entered the cage coming off an impressive upset of Rick Story in June, fell to 14-3.
Wiman makes it two in row over Danzig
All three judges scored the fight 29-28. ESPN.com also scored the fight 29-28 for Wiman.
In the first meeting between the two, on June 12, 2010, Wiman submitted Danzig in the opening round.
"It was good to be on the other end [of a decision]," said Wiman, who lost a disputed unanimous decision to Dennis Siver in July. "I am glad that I got it this time."
Wiman improved to 14-6. Danzig slipped to 20-9-1.
Franklin McNeil covers mixed martial arts and boxing for ESPN.com. Follow him on Twitter at www.twitter.com/Franklin_McNeil.