They also achieved their first objective, which was to avoid a repeat of their dismal first round exit at the last World Cup, as they booked a place in the round of 16 with a game to spare.
Spain have won both of their games in Group D without conceding a goal and Turkey have lost theirs without scoring.
Angry Turkey coach Fatih Terim said his team made an unbelievable mistake on one goal and accused them of throwing in the towel.
His opposite number Vicente del Bosque was pleased that his side had been more clinical in the penalty area.
“It’s good to have fulfilled the first objective. We played well and controlled the game virtually for the 90 minutes,” he said. “There is no point in playing well on the rest of the pitch if we can’t finish.”
Turkey made a reasonably positive start but fell apart after Morata, criticised for being ineffective in the 1-0 win over Croatia, and Nolito struck in quick succession before halftime.
Spain virtually walked the ball into the net for the third, Morata tapping home after Iniesta threaded one of the best passes of the tournament through a bewildered Turkish defence.
“The first 30 minutes was okay but then we conceded two goals by making some individual mistakes, one of them was unbelievable,” said Terim.
“Our national team threw in the towel, I have never accepted this and I will never accept it. I am deeply upset,” he added.
Iniesta, passing immaculately as always, orchestrated Spain’s midfield, assisted by Nolito and David Silva, as his side gave the most dominant performance of the finals so far.
Turkey captain Arda Turan had another low-key game and, for a period during the second half, was jeered by the Turkish fans every time he touched the ball.
Spain began in their usual style, patiently probing for an opening and got the breakthrough after 34 minutes when a passing move down the left ended with Nolito swinging a cross into the area and Morata squeezed between two defenders to head home.
Spain struck again three minutes later, helped by a mistake from Mehmet Topal.
Cesc Fabregas lifted a pass into the area and, although Topal got his head to it, he could only send the ball backwards towards Nolito, who slotted past Babacan.
Spain were toying with their opponents by now and struck again just three minutes into the second half.
Iniesta advanced, then produced his geometrically perfect pass to Jordi Alba, who touched it to Morata for a simple third.
Spain then eased off, passing the ball nonchalantly for long spells while the Turkish fans vented their wrath on Turan.
Turkey’s disappointed fans lit flares at the end of the game, filling one corner with of the ground with smoke, and will almost certainly face a UEFA disciplinary hearing.