Cristiano Ronaldo hit a record-extending 26th La Liga hat-trick for Real Madrid in their 4-1 victory away to Espanyol but Barca cannot be caught now with a four point lead.
Messi combined with Pedro Rodriguez and then slotted home from the centre of the penalty area with 65 minutes gone.
It had been a cagey game but the talent of the Argentine shone through again to break the deadlock and help Luis Enrique to his first piece of silverware at the helm of Barcelona.
The Catalan side have dominated the list of La Liga titles in recent years and remain on course to repeat their trophy treble of 2009.
They are through to the Champions League final on June 6 to face Juventus and will play Athletic Bilbao in the King's Cup showpiece on May 30.
"Last year was tough for us and we were not good enough to be champions but this year we are doing well,” midfielder Sergio Busquets told reporters.
"This is the first trophy for us and we are going to celebrate it as it is the most difficult tournament because we face all the teams.
"It is the most important although the Champions League is the most prestigious," he added.
Barcelona were missing Luis Suarez from their devastating attacking trio due to a hamstring injury with Pedro stepping into the forward line.
Atletico provided their usual aerial threat and keeper Claudio Bravo clawed away a Jose Maria Gimenez header from a corner early on while Messi wasted a golden chance with a weak header in front of goal that went straight to keeper Jan Oblak.
The game settled into a contest where Barca had plenty of possession, but lacked precision in the final third of the pitch, against an Atletico side that looked to soak up the pressure.
The gaps were beginning to emerge in the Atletico backline as Barca continued to press and Messi found space after playing a one-two with Pedro before finding the back of the net.
Minutes later Messi assisted Neymar who could have doubled their advantage but the Brazilian’s shot flew over the crossbar.
Ronaldo showed his typical competitiveness as he lifted Real to victory in the second half against Espanyol despite the La Liga title escaping their grasp.
The Portuguese now has two more hat-tricks overall in the league than Messi and he also leads this season’s scoring charts with 45 La Liga goals, four more than the Argentine.
Real looked low on morale during the first 45 minutes following their Champions League elimination last Wednesday by Juventus but Ronaldo put them ahead after being found by Karim Benzema on the hour.
While Cristian Stuani pulled a goal back for Espanyol, Marcelo restored Real's lead and then Ronaldo scored twice more in the final eight minutes to seal the win.
Elsewhere in the battle for the Champions League places Valencia, in fourth, drew 1-1 with Celta Vigo and Sevilla a point below them in fifth beat Almeria 2-1.
(Writing by Tim Hanlon in Barcelona and Iain Rogers, editing by Alan Baldwin)
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