Messi started on the bench ahead of Wednesday's UEFA Champions League semi-final first leg against Liverpool, but he was required at the start of the second half with the score still goalless.
Barca needed a win to end the challenge of nearest rivals Atletico Madrid, who now trail by nine points with three matches remaining and cannot catch the Blaugrana because of the two sides' head-to-head record.
This title is a landmark one for Messi:
Barca Need Summer Overhaul Despite Another Title Win
Winning a second title in a row, and an eighth in the last 11 seasons, looks good in both the record books and trophy cabinet. What the achievements can't do is mask the decline of this Barcelona squad.
Manager Ernesto Valverde and club president Josep Maria Bartomeu can't be fooled into thinking this title means an overhaul isn't needed this summer. Instead, the Blaugrana need an infusion of fresh talent.
It said everything that Valverde had to bring Messi off the bench at half-time to beat La Liga's 15th-placed team at home.
The team is too reliant on Messi for inspiration and is ageing at key positions or not good enough at others.
The latter problem can be summed up by Philippe Coutinho's inability to exert his influence during Messi's initial absence:
Then there was the sight of Ousmane Dembele slipping to end more than one break forward. The Frenchman is capable of brilliance, but he's also too often guilty of the ridiculous.
Two big-money transfer misfires made Barca blunt without Messi and further underlined the meagre supporting cast around the main man.
It didn't help that Luis Suarez was also having an off night, which has also been far from a rare occurrence this season.
Messi eventually showed them how it's done, but Barca's problems weren't just limited to struggles in attack. The defence looked vulnerable, as Levante wingers Jose Luis Morales and Jason both spurned excellent chances when allowed to run through on goal.
Ageing is a big part of Barcelona's problems at the back. Gerard Pique is still easily the best centre-back on the books, but he's also 32, while left-back Jordi Alba is 30.
It's a similar story in midfield, where Sergio Busquets, the only natural holding player in the squad, is 30. Meanwhile, 31-year-old former Juventus and Bayern Munich man Arturo Vidal looks increasingly out of place at a club that traditionally favours artistry over industry.
With Suarez also 32, this summer is the ideal time for Barca to undertake some wide-scale retooling. It's a necessity if this club is going to keep its status as Spain's best and one of the heavyweights in the Champions League for much longer.
Barcelona welcome Liverpool on Wednesday, while Levante will host bottom-of-the-table Rayo Vallecano on Saturday.