Thiem, 24, had underlined his credentials to claim the French Open with a straight sets win over the 10 time champion Rafael Nadal in the last eight in Madrid on 11 May.
The Austrian then backed up that exploit with a convincing 6-4 6-2 victory over the sixth seed Kevin Anderson in the semi-final 24 hours later.
But second seed Zverev was a bridge too far. The German 21-year-old is touted as a future world number one and he displayed patience, power and poise to outmanoeuvre his Austrian adversary.
The victory in 79 minutes furnished him with his third title at a Masters 1000 event - esteemed just below the four Grand Slam tournaments.
Last year Zverev beat Novak Djokovic to hoist the Rome Masters and a few months later outwitted Roger Federer to lift the Montreal Masters.
In both of those encounters, he was facing one of the grand wizards of the tour and entered the contest as the aspiring apprentice. In Madrid on Sunday he was the higher seed and facing one of his contemporaries. He rose to the challenge.
He broke the fifth seed at the start of each set and, aided by the quickness of the courts, his serve was almost untouchable in the opening set.
"I've really worked hard on my service," said Zverev after his triumph. "Dominic is one of the best returners out there. But I was confident I could handle the pressure.
"This is my third Masters. I'm just 21 and I'm really more than fortunate," he added.