The Spaniard was irrepressible at times as Gerardo Martino's men overcame a sluggish start to put themselves in the driving seat in this Copa del Rey quarterfinal.
After a sluggish start, and falling a goal behind courtesy of Nabil El Zhar's effort, which once again exposed Barca's defensive frailties, the visitors turned on the style.
Cristian Tello scored a hat trick and, although Messi did not get on the scoresheet in his 400th appearance for the club, he would have been more than delighted with the three assists he laid on for the Spaniard.
However, while Barca finished on top it was submissive to a bright start from the hosts, who were clearly buoyed by their 1-1 draw Gerardo Martino's men on Sunday.
Both sides made a whole host of changes from that match, and it was Levante who took the game to Barca in the early stages.
However, Barca nearly scored with its first attempt on goal as Pedro cut inside from the right and curled a delightful effort that cannoned off the post, before Loukas Vyntra had to be alert moments later to snuff out a dangerous ball across from the lively Tello.
The Catalans continued to press and Messi played a delicate ball in behind the Levante defense, finding the run of Adriano, but the Brazilian's looping effort narrowly went wide.
But it was Levante who took the lead and deservedly so. The Blaugrana's defensive frailties from set pieces were exposed once again as Carles Puyol failed to get purchase on a clearance, allowing El Zhar to power a shot toward goal; Jose Pinto reacted well, but the winger followed up his own effort to prod home.
Messi attempted to restore parity as Dani Alves fed him the ball and the Argentine tried to shape an effort around a cluster of bodies, but his shot did not test Javi Jimenez.
However, the Liga champions equalized following calamitous defending from the hosts. Messi delivered a ball over the top, finding Tello in space, and his weak shot squirmed loose of Jimenez's grasp, with Vyntra's attempted clearance cannoning in off Juanfran.
It became worse for the hosts as it was another incisive pass from Messi who found Tello again as the hosts struggled to cope with the Spaniard's blistering pace, and he slipped the ball past Jimenez to turn the game completely on its head.
Messi came close with an effort from just inside the box, while Xavi forced a reflex save from the Levante shot stopper, but it was Tello, assisted by Messi, who fired past Jimenez.
Barca wrapped the game up when Messi found Tello with a delightful dink over the top, which exposed the vulnerability of the Levante defense, and the Spaniard, full of confidence, took a touch before firing a volley emphatically past Jimenez.