The South Korea star pulled up holding his hamstring as he chased a long ball over the top in the opening 20 minutes at Emirates Stadium and he had to be replaced by Erik Lamela.
Son immediately dropped to ground and quickly became clear he had suffered an injury.
Spurs now face an anxious wait to discover the extent of the problem but they face the prospect of being without Son for at least a few weeks.
Son has been a vital player for Tottenham this season, scoring 13 goals in 27 Premier League appearances.
The 28-year-old was making his 43rd appearance of the season on Sunday and Jose Mourinho will fear the gruelling season has caught up with him.
Son has only scored two Premier League goals in 2021 but he has started to form formidable front three for Tottenham with Harry Kane and Gareth Bale.