Electronic learning (e-learning) has become one of the widely used modes of pedagogy in higher education today due to the convenience and flexibility offered in comparison to traditional learning activities. Advancements in Information and Communication Technology have eased learner connectivity online and enabled access to an extensive range of learning materials on the World Wide Web. Post covid-19 pandemic, online learning has become the most essential and inevitable medium of learning in primary, secondary and higher education. In recent times, Massive Open Online Courses (MOOCs) have transformed the current education strategy by offering a technology-rich and flexible form of online learning. A key component to assess the learner's progress and effectiveness of online teaching is the Multiple Choice Question (MCQ) assessment in most of the MOOC courses. Uncertainty exists on the reliability and validity of the assessment component as it raises a qualm whether the real knowledge acquisition level reflects upon the assessment score. This is due to the possibility of random and smart guesses, learners can attempt, as MCQ assessments are more vulnerable than essay type assessments. This paper presents the architecture, development, evaluation of the I-Quiz system, an intelligent assessment tool, which captures and analyses both the implicit and explicit non-verbal behaviour of learner and provides insights about the learner's real knowledge acquisition level. The I-Quiz system uses an innovative way to analyse the learner non-verbal behaviour and trains the agent using machine learning techniques. The intelligent agent in the system evaluates and predicts the real knowledge acquisition level of learners. A total of 500 undergraduate engineering students were asked to attend an on-Screen MCQ assessment test using the I-Quiz system comprising 20 multiple choice questions related to advanced C programming. The non-verbal behaviour of the learner is recorded using a front-facing camera during the entire assessment period. The resultant dataset of non-verbal behaviour and question-answer scores is used to train the random forest classifier model to predict the real knowledge acquisition level of the learner. The trained model after hyperparameter tuning and cross validation achieved a normalized prediction accuracy of 85.68%.