You can take advantage of method similar to presented in Y14.5-2009 fig. 4-30. Just forget about datum feature B and 2 holes shown there.
If the flat is not critical to functionality of the shaft you can use less elegant method (in my opinion), that is simply apply two directly toleranced dimensions: 1) for shaft diameter, 2) between flat and the opposite side of the shaft.
Since this looks to be relatively long feature, you may want to condiser control of straightness of derived median line of the shaft as shown in fig. 5-3 (Y14.5-2009).
As a matter of fact you did not write anything about your major functional concern for this application, so please just treat my answer as a suggestion.