The world's most expensive footballer had been a doubt for this summer's World Cup in recent months due to an injury, but he showed few signs of rust with a fine solo effort to fire Tite's side to the win on Merseyside.
It was the 26-year-old's moment of magic which proved to be the main difference in an otherwise even game, although Brazil did add a second with the last kick of the contest as Roberto Firmino scored on his club ground to cap off the victory.
Brazil are now unbeaten in their last 10 matches going into their final World Cup warm-up game against Austria next weekend, whereas Croatia will take on Senegal on Friday in their last outing before the tournament gets underway.
Neymar started on the bench as his recovery from a broken metatarsal continued, but Philippe Coutinho was named in the starting lineup for his first return to Anfield since leaving Liverpool for Barcelona in January.
It was another player familiar with the Merseyside surroundings who had the first chance of the game, though, as Dejan Lovren climbed highest inside the penalty area to plant a firm header narrowly wide of the target.
Brazil would not have been able to have any complaints at going behind after a slow start, and it looked as though things might get worse for them when captain Thiago Silva was caught by a high challenge from Andrej Kramaric which may have resulted in a red card during a competitive fixture.
Silva was fine to continue after treatment, but moments later he exchanged passes with Miranda, who gifted possession away in a dangerous area and it was left to Alisson Becker to bail his defenders out with a low save from Ante Rebic's resulting effort.
Coutinho was limited to a couple of long-range efforts in the first half, neither of which threatened Danijel Subasic in the Croatian goal.
The best chances continued to fall to Croatia, with Ivan Perisic laying the ball off to Kramaric, who completely missed his kick from inside the area before Marcelo was called into defensive action at the back post twice in quick succession.
Brazil's best attacking moment of the first half arrived shortly after the half-hour mark when Willian's shot/cross was cleared away from inside the six-yard box, and the closing stages of the half were disrupted by a number of free kicks, with referee Michael Oliver producing three first-half yellow cards.
Tite turned to Neymar during the interval in an effort to provide the sort of inspiration which was sorely lacking in the opening 45 minutes, with the Paris Saint-Germain forward replacing Fernandinho for his first taste of competitive action in more than three months.
The attacking change allowed Brazil to take more control over the game, but clear chances were still difficult to come by and the closest they came in the first 10 minutes of the second half was a 30-yard strike from Marcelo which fizzed narrowly past the post.
It wasn't until the 57th minute that Brazil had their first shot on target, and it was no surprise that it came from Neymar when he cut inside before forcing Subasic into a routine save with a curling effort towards the far top corner.
A raft of substitutions disrupted the rhythm of the second half, but Croatia did create another chance to take the lead shortly before the hour mark when Rebic peeled off his marker and glanced a header towards the bottom corner which left Alisson scrambling to push it away.
It was the returning Neymar who stole all the headlines, though, as he marked his first appearance in more than three months with a trademark goal to take his tally for Brazil up to 54 - just one behind Romario on the all-time list.
Willian and Coutinho combined to find the Paris Saint-Germain winger, who embarked on a mazy run inside the box before blasting an unstoppable finish in off the underside of the crossbar.
It looked as though Neymar's moment of magic would prove to be the decisive factor as Croatia struggled to come up with a response, and Brazil looked the most like adding to the scoring in the closing stages when Neymar again came close with a free kick and Firmino flashed an effort wide of the near post.
The Anfield crowd were treated to a goal from the Liverpool favourite right at the death, though, as Firmino collected Casemiro's cross on his chest before holding off a challenge and lifting his finish over the keeper from inside the area.
There was barely even time for the restart as Brazil ran out winners in their opening warm-up game, with their World Cup campaign getting underway against Switzerland in June 17 before subsequent group games against Costa Rica and Serbia.
Croatia, meanwhile, have been drawn in a group alongside Nigeria, Argentina and Iceland as they bid to make it into the knockout stages for the first time since 1998.
BRAZIL (4-3-3): Alisson; Danilo, Silva, Miranda (Marquinhos 65'), Marcelo (Luis 60'); Paulinho, Casemiro, Fernandinho (Neymar 46'); Willian (Fred 82'), Jesus (Firmino 60'), Coutinho (Taison 82')
CROATIA (4-2-3-1): Subasic; Vrsaljko (Jedvaj 87'), Corluka (Caleta-Car 52'), Lovren, Vida; Badelj (Brozovic 61'), Rakitic (Bradaric 83'); Rebic (Pjaca 64'), Modric (Kovacic 58'), Perisic; Kramaric