The Mexican moved up a division to beat Englishman Rocky Fielding inside three rounds last year, becoming a three-weight world champion, but returned to 160 pounds to face Jacobs for the unified world middleweight titles.
Alvarez busily got to work on his opponent in the early rounds, firing off jabs to the 32-year-old's body, although the American started to land his own punches in the second round.
The onslaught continued with Alvarez landing uppercuts in the third and fourth rounds, while Jacobs struggled to keep up with the 28-year-old's skill and movement.
The American started to come out on top through rounds seven and eight and there was more action in round nine as both men exchanged shots, Jacobs connecting a heavy hook on Alvarez's chin near the bell.
Jacobs held on through all 12 rounds but Alvarez's early dominance left little doubt he would be crowned the winner, with the fight scored 115-113, 115-113, 116-112 in his favour.
Quoted on Sky Sports, Alvarez said after the fight: "It's just what we thought, we knew he was going to be a difficult fighter."
In relation to the heavy left hook he took in the ninth, he added: "It was a hard shot, I went to the corner and said no big deal."
Having drawn with Gennady Golovkin in their first bout in 2017, Alvarez beat the Kazakhstan fighter last September, and said he would be open to a third bout.
"I'm just looking for the biggest challenge and I want that to be my biggest fight.
"For me, we're done, but if he wants to do it again, I'll beat him again."
Jacobs admitted the early rounds set him back, but thought victory could have been in sight.
"He's a tremendous champion, I take my hat off to him," said Jacobs.
"I definitely think it took me a couple of rounds to get my wits about me.
"I feel like I gave enough to get the victory, but I've got to go back to the tapes and see what happened."
