The visitors had yet to suffer a defeat in World Cup qualification but did in Seoul following a second-half comeback from Hong Myung-Bo's men.
The visitors opened the scoring in the seventh minute of the friendly encounter in Seoul when Pajtim Kasami hit a sweetly struck, drilled effort from distance low into the back of the net.
But South Korea fought its way back into the match and was on level terms 14 minutes after the break when Hong Jeong-Ho headed beyond Diego Benaglio from a corner.
And the hosts struck the winner three minutes from time as Chung-Yong headed home a Lee Keun-Ho cross.
The result earned South Korea its first back-to-back victories for 15 months, while Switzerland's 14-match unbeaten run came to an end. Hong Myung-Bo's men next face a trip to Dubai on Tuesday to meet a Russia side that is unbeaten in its last four.