Guerrero (31-1-1, 18 KOs) floored the former 147-pound champion in the first round and again in the second round before persevering through a physically punishing bout. Berto's eyes were both swollen shut by the final bell, and Guerrero's right eye was nearly closed after multiple rounds of close-range punching.
"I did tell Andre I was going to beat him down, so I had to be a man of my word," Guerrero said. "But he did defend himself like a true champ. ... I had to get on the inside with him, work his body and fight him on the inside."
Guerrero, the former champion at featherweight and super featherweight from Gilroy, Calif., called out Floyd Mayweather Jr. after the fight. Guerrero and Mayweather both have promotional relationships with Golden Boy, making a matchup possible.
"Pretty Boy, let's do it," Guerrero said.
Berto (28-2) recovered from a slow start to test Guerrero despite a closed right eye from the second round onward. Guerrero took significant damage, but hung on for his eighth consecutive win.
All three judges at Citizens Bank Business Arena scored the bout 116-110 for Guerrero.
Returning to the ring for his first fight in 14 months, Berto complained about the officiating after his second loss in three outings. Berto failed a doping test earlier this year, wiping out a lucrative rematch with Victor Ortiz.
"I just didn't understand," Berto said. "He was coming in, grabbing and holding me. Every time I tried to get off, the referee kept warning me for shots. ... At the end of the day, Robert fought a good fight and he got the win. If you want to do it again, we'll definitely do that."
Guerrero landed 35 percent of his 731 punches, while Berto connected with 44 percent of his 411 blows, including 50 percent of his power punches.
Guerrero dropped Berto with a left hand over Berto's defense and a series of additional left hands while a dazed Berto attempted to hold. Guerrero also appeared to use his right hand to keep Berto close during the flurry, but wasn't called for a hold.
Berto went down again in the opening seconds of the second round when Berto connected with a body shot and a left uppercut. Berto, whose eye was injured by a left cross moments earlier, gathered himself and clutched his way through the rest of the round, although Berto's corner also complained about Guerrero's tactics.
Berto picked up his aggression in the middle rounds, catching Guerrero with uppercuts and hooks. Both fighters traded big shots in the 12th round, which ended with Guerrero and Berto both claiming victory.
"He didn't hurt me at all," Guerrero said. "I took some good shots from him. He's a strong guy, punched hard, but I've got a good chin."
On the undercard, rising 154-pounder Keith Thurman battered Carlos Quintana and eventually stopped the veteran with 41 seconds left in the fourth round. Thurman (19-0, 18 KOs) knocked down Quintana in the first round with a hook to the body and never stopped pursuing Quintana, with referee Jack Briggs eventually stopping the bout with Quintana nearly out on his feet.