Network Traffic Classification enables a number of practical applications ranging from network monitoring to resource management, with security implications as well. Nowadays, traffic classification has become a challenging task in order to distinguish among a variety of applications due to the huge amount of generated traffic. Therefore, developing Machine Learning (ML) models, which can successfully identify network applications, is one of the most important tasks. However, among the ML models applied to network traffic classification so far, no model outperforms all the others. To solve these issues, this paper proposes a novel Deep Learning (DL)-based approach that incorporates multiple Decision Tree based models. This approach employs a non-linear blending ensemble method by combining tree-based classifiers through DL in order to maximize generalization accuracy. This ensemble consists of two levels called base classifiers and meta-classifiers. In the first level, Decision Tree-based models are used as the base classifiers while in the second level, DL is used as a meta-model to combine the outputs of the base classifiers. Using two publicly available datasets, we show that our proposed ensemble is suitable for network traffic classification and outperforms the linear blending (using logistic regression as meta-model) as well as several well-known ML models, which are Support Vector Machine (SVM), Decision Tree (DT), Random Forest (RF), Multi-Layer Perceptron (MLP), AdaBoost, K-Nearest Neighbors (KNN), LightGBM, Catboost, and XGBoost.