High-resolution aerial imagery can provide detailed and in some cases even real-time information about traffic related objects. Vehicle localization and counting using aerial imagery play an important role in a broad range of applications. Recently, convolutional neural networks (CNNs) with atrous convolution layers have shown better performance for semantic segmentation compared to conventional convolutional aproaches. In this work, we propose a joint vehicle segmentation and counting method based on atrous convolutional layers. This method uses a multi-task loss function to simultaneously reduce pixel-wise segmentation and vehicle counting errors. In addition, the rectangular shapes of vehicle segmentations are refined using morphological operations. In order to evaluate the proposed methodology, we apply it to the public “DLR 3K” benchmark dataset which contains aerial images with a ground sampling distance of 13 cm. Results show that our proposed method reaches 81.58 % mean intersection over union in vehicle segmentation and shows an accuracy of 91.12 % in vehicle counting, outperforming the baselines.