Earlier, Neymar, Lionel Messi and Luis Suarez were all on target to take their combined tally for the season to 102 as Barcelona kept pace at the top with a 4-1 win over Villarreal.
But the visitors were back in the contest 11 minutes later as they sprung Barca's high defensive line with a through-ball from Roberto Soldado sending Cedric Bakambu clear on goal, and the Congolese striker provided a cool finish.
"Every opponent gives you a hard game but we started the game really well and scored early", said Morata.
Any hopes of a late comeback were ended nine minutes from time when Barcelona were awarded a penalty, although replays showed that the officials were wrong to award a handball after Neymar had brilliantly set up Suarez for a shot at goal.
Since Suarez's arrival from Liverpool in 2014 saw him join Messi and Neymar at Camp Nou, the forwards have been prolific in helping Barca to silverware.
The defending champions, who lead the Spanish league on the head-to-head tiebreaker but have played one game more than Madrid, will need to be at their best on Saturday against a Villarreal team with the league's second-best defense.
Neymar opened the scoring in the first half, but it was his trickery and showboating which brought the home supporters to their feet in the second period.
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As Barcelona try to keep the heat on Real Madrid in the battle at the top, added motivation may come in looking to end Luis Enrique's reign with a third title in as many years.
That proved crucial as Messi restored Barcelona's lead four minutes later, just before half-time.
"The truth is everything looks good", Mestre said, when asked for an update on Messi's contract situation after Barca's 4-1 win over Villarreal on Saturday.
Fresh from their 3-0 Champions League semi-final first leg victory over Atletico, the Merengues will be confident of keeping pace with Barcelona at the top of the table.
It was the Argentinian's 50th goal in all competitions this season, the fifth time in his career he has achieved the feat.
But the win sent Atletico five points clear of fourth-placed Sevilla with only six left to play for.
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