Spain has the pandemic’s second-highest death toll in the world and City confirmed their manager’s mother passed away in Barcelona on Monday.
“Everyone associated with the club sends their most heartfelt sympathy at this most distressing time to Pep, his family and all their friends,” said Manchester City in a statement.
Monday’s increase of 637 coronavirus deaths means 13,055 have died in Spain.
Last month, Guardiola donated 1m euros (£920,000) to help fight the outbreak.