The gathering of the secretive and politically influential Iglesia ni Cristo (Church of Christ) in the historic district of Manila forced all schools and some government offices to close.
The Supreme Court, as well as some basketball games in the highly popular college league, were also suspended, while Manila's governing authority urged private employers to give their staff a paid day off to avoid the traffic.
"We really apologise for those who were inconvenienced. Maybe they can just pass this off as a minor sacrifice to help their countrymen," Iglesia ni Cristo spokesman Edwin Zaballa told AFP.
Zaballa said it was also part of year-long celebrations across the country to mark the lead-up to its centenary in 2014, and "to spread the word".
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Between two and three million people attended the event either as a church follower or aid recipient, according to Manila's police chief, Isagani Genade. The organisers estimated the crowd at between 1.5 million and two million people.
The event is one of many ostentatious displays of faith in the mainly Catholic Philippines, where religious leaders also wield heavy political influence.
In a square fronting Manila's central post office, tempers frayed during the fierce afternoon heat as men, women and children jostled while waiting for medical care offered by the group.
"This is madness. I have been here since dawn to get a free medical check-up, but I will get more sick in this heat," said factory worker Flor Kato, a 40-year-old mother of five who was complaining of chest pains.
Several people fainted due to the heat, while others simply gave up in frustration.
Founded by Felix Manalo in 1914, Iglesia ni Cristo exerts huge political influence in the Philippines, despite being outnumbered by the country's more than 75 million Catholics.