This is essentially a limitation of the underlying protobuf wire format; it only supports single-dimension arrays.
Two options leap to mind; firstly, send it as a linear array, and send the dimensions separately.
You could also represent it as a list of objects that each has an array - essentially a jagged array, but with an intermediate step.
Of the two, the first is both simpler and more efficient.
Either way, if you are sending something like intergers, you should look at "packed" encoding (available via the options property) - this can further reduce the payload for arrays etc.
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