The Paris St Germain star produced a stunning individual effort in the 68th minute of his first outing since he fractured his metatarsal playing for Paris St Germain in February.
Neymar ran behind the goal, in front of Anfield's legendary Kop End, and punched the air in obvious delight as he was mobbed by team-mates.
Neymar's goal was his 54th for his country and he needs one to reach Romario as the third most prolific Brazil striker of all time behind Pele and Ronaldo.
Liverpool striker Roberto Firmino then bagged a goal on his own home turf in injury time, to seal the victory.
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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.
Brazil coach Tite brought on Neymar for Fernandinho at the break as he stepped up his recovery from a foot injury.
There was still work to do but Neymar somehow managed to force the ball past goalkeeper Danijel Subasic and in off the cross-bar from the edge of the six-yard area.
Neymar came on at Anfield as a second-half substitute and made a swift impression with a superbly taken goal in the 69th minute as the five-times world champions warmed-up for this month's tournament in Russian Federation.
Despite the looming spectre of the World Cup, now less than two weeks away, the game proved a physical one.
Brazil have Neymar on the bench and he is expected to come on at half time. It was only through Neymar's introduction that this was addressed.