This study is primarily focused on assessing the students' logical thinking and cognitive levels in an online collaborative environment. The aim is to investigate whether the online collaboration has significant impact to the students' cognitive abilities. The assessment of the logical thinking involved the use of the online Group Assessment Logical Thinking (GALT) test that has been conducted in two phases; before and after the online collaborative activities. The sample of respondents for this study is sixty first year Diploma in Computer Science students from Universiti Teknologi MARA (UiTM) Perlis, Malaysia where they were divided into fifteen collaborative groups. These collaborative groups were then engaged in a 3-hour session of collaborative activities via the Online Collaborative Learning System (OCLS). The results for this study has revealed that the online collaborative learning has significant impact to the students' logical thinking levels with the increment of 21.7% high logical thinkers with p-value<0.05 (sig. 2-tailed). Meanwhile, the investigation of the students' cognitive levels is being done by monitoring the students' abilities to solve the given questions via OCLS. The questions have been previously constructed according to the Bloom's taxonomy cognitive domain. The results have also revealed that the students at the early stage of learning programming are able to solve complex programming problems at the cognitive level Application and Analysis. There was also a strong correlation between students' logical thinking skills with their abilities to solve problems in an online platform with r = 0.631, significant at 0.012.