Global navigation satellite systems (GNSS) underpin a number of modern life activities, including applications demanding positioning accuracy at the level of centimetres, such as precision agriculture, offshore operations and mining, to name a few. Precise point positioning (PPP) exploits the precision of the GNSS signal carrier phase measurements and may be used to provide the high accuracy positioning needed by these applications. The Earth's ionosphere is critical in PPP due to its high variability and to disturbances such as scintillation, which can affect the satellite signals propagation and thereby degrade the positioning accuracy, especially at low latitudes, where severe scintillation frequently occurs. This manuscript presents results from a case study carried out at two low latitude stations in Brazil, where a dedicated technique is successfully applied to mitigate the scintillation effects on PPP. The proposed scintillation mitigation technique improves the least square stochastic model used for position computation by assigning satellite and epoch specific weights based on the signal tracking error variances. The study demonstrates that improvements in the 3D positioning error of around 62-75% can be achieved when applying this technique under strong scintillation conditions. The significance of the results lies in the fact that this technique can be incorporated in PPP to achieve the required high accuracy in real time and thus improve the reliability of GNSS positioning in support of high accuracy demanding applications.