Ionospheric irregularities remain as a challenging concern among space scientists and engineers as it can pose severe threats to satellite-based services by introducing amplitude and phase scintillations in the transionospheric radio signals. The scintillations may cause degradation of the positioning, navigation, and timing (PNT) services or even complete system failure under extreme conditions. The present work focuses on understanding the ionospheric irregularities during the space weather event on May 12, 2021, witnessing the first strong geomagnetic storm in the 25th solar cycle. This particular event commenced around 13.00 UT, apparently altering the regular development of equatorial plasma bubbles around the local post-sunset terminator. We selected three global positioning system (GPS) stations, one at the near-magnetic equator (CUSV) and two at far low-latitude locations with a longitudinal separation (THKK and HWKS) over the Southeast Asian longitudes to investigate the characteristics of ionospheric plasma irregularities on the storm day. The results showed that the amplitude of ROTI was highest at the low-latitude CUSV, followed by the THKK and HKWS stations. The increased ROTI at CUSV is due to its latitudinal location close to the geomagnetic equator in the equatorial ionization anomaly (EIA) region which often witnesses more fluctuations than the inter-mediate latitudes. The strong TEC fluctuation occurrences were comparatively minimal at HWKS station on the storm day (May 12, 2021), whereas both intermediate and relatively higher TEC fluctuation occurrences were found at THKK and CUSV stations, respectively. Moreover, the occurrence rate of moderate irregularities was the highest at CUSV, followed by THKK and HKWS, while that of weak irregularities was maximum at HKWS, followed by THKK and CUSV. This happens because the systematic longitudinal time delay observed at the onset of ionospheric scintillations corresponds to the rise of PBs velocity at the magnetic equator that strongly depended upon the F-region dynamo electric fields in the east–west direction. Furthermore, the three-dimensional (3-D) positioning errors were estimated at a 30-sec interval to understand the impact of storm-induced irregularity on the positioning solution. An excellent agreement is realized between the ROTI pattern and positioning errors at all stations, irrespective of latitudinal extent from the magnetic equator. In order to model the amplitude of the scintillation index against the SNR measurements, the linear, quadratic, and cubic regression curve fittings are utilized that indicate the cubic polynomial manifesting the best fitted SNR measurements with the weak as well as moderate scintillation index. The continuous wavelet transformation (CWT) method was implemented to mitigate the ionospheric scintillation effects on positioning accuracy. The CWT estimation reveals the hidden information in positioning error due to the scintillation index, which makes it easy to understand the ionospheric scintillation effects on positioning. The attempt in this work is aligned with the efforts towards reliable PNT operations over equatorial and low latitudes.