It was the perfect tonic for Barca following the news that coach Tito Vilanova had to have throat surgery last Thursday.
The 44-year-old was released from hospital earlier on Saturday and was absent from Valladolid's Jose Zorrilla stadium as Barca racked up a record 16th win in 17 games this season.
Real's woes deepened after the stuttering champions suffered a second consecutive setback following last weekend's 2-2 draw at home to Espanyol.
Mourinho told a post-match news conference Real were "facing an insurmountable gap" but dismissed a question about whether he feared for his job.
"Football is football, why should I fear for my job?" the Portuguese said.
"We coaches know perfectly well that football has no memory. The titles you have won don't count, the work you have done doesn't count.
"Losing always hurts but it hurts me more when you don't give what you are able to give.
"In the brief chat I had with the players I told them they can go home sad at losing but in the knowledge that they did their job to the best of their ability."
Atletico, resurgent under Argentine coach Diego Simeone, have 40, with Real on 33 and Malaga, who are coached by Mourinho's predecessor at Real, Manuel Pellegrini, on 31.
Messi uncharacteristically fluffed a simple chance early in the second half but the Argentine World Player of the Year doubled Barca's lead in the 59th minute with a trademark run and finish.
Xavi's clever backheel set the Argentine on his way and Messi dinked the ball between a defender's legs before firing a low shot into the far corner.
It was his 26th La Liga goal of the campaign and his 91st of 2012, extending the calendar year record he broke earlier this month when he overhauled Gerd Muller's 40-year-old mark of 85.
Barcelona's assistant coach Jordi Roura has taken charge on a temporary basis until Vilanova, who is starting a course of chemo- and radiotherapy, is well enough to return.
"We are on a good run and we
