Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the most important viruses affecting global grape and wine production. GLRaV-3 is the chief agent associated with grapevine leafroll disease (GLRD), the most prevalent and economically destructive grapevine viral disease complex. Molecular response of grapevine to GLRaV-3 infection is poorly characterized, limiting the understanding of GLRaV-3 pathogenesis and viral-associated symptomatic development. In this research, we used RNA Sequencing (RNA-Seq) to profile the global gene expressional change of Cabernet Franc, a premium red wine grape, analyzing leaf and berry tissues at three key different developmental stages. We have identified 1,457 differentially expressed genes (DEGs) in leaves and 1,181 DEGs in berries. Expressional profiles of a subset of DEGs were validated through RT-qPCR, including those involved in photosynthesis (VvPSBP1), carbohydrate partitioning (VvSUT2, VvHT5, VvGBSS1, and VvSUS), flavonoid biosynthesis (VvUFGT, VvLAR1, and VvFLS), defense response (VvPR-10.3, VvPR-10.7), and mitochondrial activities (VvETFB, VvTIM13, and VvNDUFA1). GLRaV-3 infection altered source-sink relationship between leaves and berries. Photosynthesis and photosynthate assimilation were inhibited in mature leaves while increased in young berries. The expression of genes involved in anthocyanin biosynthesis increased in GLRaV-3-infected leaves, correlating with interveinal reddening of leaves, a hallmark of GLRD symptoms. Notably, we identified changes in gene expression that suggest a compromised sugar export and increased sugar retrieval in GLRaV-3-infected leaves. Genes associated with mitochondria were down-regulated in both leaves and berries of Cabernet Franc infected with GLRaV-3. Results of the present study suggest that GLRaV-3 infection may disrupt mitochondrial function of grapevine leaves, leading to repressed sugar export and accumulation of sugar in photosynthetic tissues. The excessive sugar accumulation in GLRaV-3-infected leaves would trigger downstream GLRD symptom development and negatively impact berry quality. We propose a working model to account for the molecular events underlying the pathogenesis of GLRaV-3 and symptom development. A refined total RNA extraction protocol suitable for dark-skinned ripe berries and novel reference genes suitable for grapevine-associated RT-qPCR analysis were identified during the course of this research.