Wind gave the monicker "Amen Corner" to holes 11, 12 and 13 because of the seemingly miraculous way in which Palmer played those holes on the final day.
The official website of The Masters describes the happenings this way:
"Saturday evening in 1958, heavy rains soaked the course. For Sunday’s round, a local rule was adopted allowing a player whose ball was embedded to lift and drop it without penalty. Sunday on No. 12, Arnold Palmer hit his ball over the green and the ball embedded in the steep bank behind it. Being uncertain about the applicability of the local rule, the official on the hole and Palmer agreed that the ball should be played as it lay and that Palmer could play a second ball which he dropped. Palmer holed out for a 5 with the original ball and a 3 with the second ball. The committee was asked to decide if the local rule was applicable and if so, which score should count.
"At No. 13, still unsure of what his score was at 12, Palmer sank an 18-foot putt for eagle 3. When he was playing No. 15, Palmer was told his drop at 12 was proper and that his score on the hole was 3, leading to his first major victory."
Wind's inspiration for the name "Amen Corner" came from a jazz record titled "Shouting at Amen Corner."
(And how did the writer of that jazz song come up with "Amen Corner"? That answer here.)
