The result at Camp Nou means Ernesto Valverde's men sit nine points ahead of nearest rival Atletico Madrid, against whom they boast a superior head-to-head record, with three games to go.
Barca still has the chance to lift two more trophies, with a UEFA Champions League semi-final against Liverpool and a Copa del Rey final with Valencia to come.
Valverde's decision to again leave Messi on the bench, perhaps with an eye on Thursday's (AEST) first-leg visit of Liverpool, will have provided some initial comfort to the visitors.
In the reverse fixture, the star forward was involved in all of Barca's goals, scoring three and assisting two, as the defending champion ran out a 5-0 winner.
But he was introduced at the break and made the difference, showing profligate team-mates Philippe Coutinho and Luis Suarez the way.
Levante might have hoped for an easier outing in Messi's first-half absence, but goalkeeper Aitor Fernandez, who did not play in that match, was pressed into notable action twice inside the opening five minutes to repel efforts from Suarez and Coutinho.
The same pair was denied again, Suarez at the near post and Coutinho with a gilt-edged headed chance, before the Brazilian struck the crossbar with a free-kick.
Messi came on for the wasteful Coutinho at the interval and finally made the breakthrough just past the hour mark, with Levante failing to clear their lines and the Argentina striker supplying a two-touch finish from the edge of the six-yard box.
Levante was stung into action and Jose Luis Morales should have levelled matters soon after, but he skied over the bar with under-worked Marc-Andre ter Stegen left exposed.
Considering its complete lack of attacking threat for more than an hour, Levante did well to make the closing stages interesting and Enis Bardhi struck the post in a late scramble, but Barca ultimately sealed the three points it needed to celebrate an eighth LaLiga title in 11 seasons.