Digital holography is a well-established technology for optical quality control in industrial applications. Two common challenges in digital holographic measurement tasks are the ambiguity at phase steps and the limited depth of focus. With multiwavelength holography, multiple artificial wavelengths are used to extend the sensor’s measurement range up to several millimeters, allowing measurements on rough surfaces. To further extend the unambiguous range, additional highly stabilized and increasingly expensive laser sources can be used. Besides that, unwrapping algorithms can be used to overcome phase ambiguities—but these require continuous objects. With the unique feature of numerical refocusing, digital holography allows the numerical generation of an all-in-focus unambiguous image. We present a shape-from-focus algorithm that allows the extension of the depth of field beyond geometrical imaging limitations and yields unambiguous height information, even across discontinuities. Phase noise is used as a focus criterion and to generate a focus index map. The algorithm’s performance is demonstrated at a gear flank with steep slopes and a step sample with discontinuities far beyond the system’s geometrical limit. The benefit of this method on axially extended objects is discussed.