Shuffling: Purpose and formal definition
In side channel, shuffling makes correlation attacks harder. For example, if you shuffle the 16 AES S-Boxes in the first round each execution, and you target say first S-Box' output in the attack, at any single point in the trace you will see information related directly to that output only on 1/16th of all traces, and in the other 15/16th traces there will be something else, which qualifies as &quot;noise&quot; for the attack.
Note that this countermeasure is rather weak and is mostly considered complimentary to more sound masking countermeasure. Indeed, after taking 16 times more traces (maybe a bit more), the correlation would become noticeable again. While this adds up to the practical attack complexity, it is impossible to achieve exponential complexity increase, as masking allows.