This article compares two intelligent methods for automatic detection of unbalancing, cracks, and parallel misalignment in rotary machines. The finite element method is used to model the faults in a rotating system. The modeled system then operates virtually under different conditions in the steady-state operation; the vibrational responses are calculated numerically. To compare the accuracy of different manners in the classification of defective systems, firstly, four distinct types of features, i.e., statistical, frequency, time–frequency, and uncertainty are exploited. The T test process is utilized to test the extracted characteristics; the unreliable features are removed from feature vectors, then the remained ones are used in four supervised machine learning classifiers, i.e., support vector machine, k-nearest neighbors, Naive Bayes, and decision trees. In the following, as the convolution neural networks (CNNs) approach, the persistence spectrums of raw signals are plotted, and these graphs are introduced as input data. Comparing results of the different classification methods, it has been observed that although CNNs based on persistence spectrum graphs are computationally heavy and time-consuming, they provide more accurate results than the other classifiers. The results show that the proposed approach for rotor fault detection is effective, accurate, and robust and that it has promise for real engineering applications.