Ted Durcan, on the tiny Italian Derby winner, tracked Frankie Dettori on Sheikh Mohammed's leading hope, before getting on top in the final furlong to win by three-quarters of a length.
The result was a massive shot in the arm for Godolphin, as Mastery was giving them their first domestic Classic since Rule of Law took the St Leger of 2004.
Sheikh Mohammed, delighted his long wait was over, said: "These are horses, not machines.
"They're flesh and blood and sometimes you have problems with them.
"Everyone at Godolphin is a team player. I'm very proud of them."
This was Durcan's second Classic, following on from Light Shift's 2007 Oaks win.
"Everyone wants to ride in races like this. To ride in one is an honour, and to win one is great," he said.
Monitor Closely was back in third.
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