Messi fractured the radial bone in his right arm after falling awkwardly in the 4-2 victory against Sevilla on Saturday and he is set to be sidelined for around three weeks.
Record signing Philippe Coutinho put Barca ahead by curling a first-time shot into the top corner in the second minute and Messi doubled the lead 10 minutes later with a thumping strike into the far corner.
But Barca were grateful to goalkeeper Marc-Andre ter Stegen for a pair of sensational double saves, while Luis Suarez and Ivan Rakitic struck in the second half to ensure a Clement Lenglet own goal and Luis Muriel's strike were mere consolations.
Atletico Madrid failed to take full advantage of their neighbors' slip up as they were held to a 1-1 draw away to Villarreal, who they have failed to beat in seven meetings.
Real Madrid was four points behind Barcelona, in fifth place.
'Car crash in slow motion' : Finch laments Australia's 'horrific' batting
Half-centuries by Alyssa Healy and Ashleigh Gardner helped Australia put up a total of 195 runs on the board in 20 overs. He praised the number one ranked T20I side in the world while also calling Australia's batting approach cocky.
Fans loudly jeered after Madrid reached 481 minutes without finding the net in the loss to Levante, which entered the game with the league's third-worst defence. Borja scored a goal in each half in Espanyol's 2-0 win away to Huesca, whose new coach Francisco debuted with a defeat after replacing Leo Franco during the global break. Marcelo pulled one back in the 72nd.
As Gareth Bale and Karim Benzema struggle to find the net, Lopetegui could do with a hero of Ronaldo's ilk for the trip to Catalunya. Barcelona, meanwhile, seem to have sparked a rival.
Barca has not won a Clasico without Messi since his debut for the club, failing to win either of the two matches with Madrid he has missed since 2004.
The Catalan giants, now sitting at the top of LaLiga, have pointed out that previous instances of Messi being injured, suspended or rested have not led to a slump in team form.
Villarreal, 14th in the standings, remained winless after six home matches in all competitions this season.
At the time, Julio Baptista's goal was the difference in a 1-0 narrow win for Real.