Neither Brunei, the Association of Southeast Asian Nations (ASEAN) chair, nor the bloc's secretary-general made a mention of the no-show in opening remarks at the virtual meeting.
The move was a rare bold step by a regional grouping known for its non-interference and engagement.
Myanmar's junta late on Monday said it would only agree to its head of state or ministerial representative attending the summit, indicating its seat would be empty.
Since overthrowing Suu Kyi's government, detaining her and most of her allies and ending a decade of tentative democracy, Myanmar's military has killed more than 1,000 people and arrested thousands, monitoring group the Assistance Association for Political Prisoners says.
On the agenda for Tuesday's opening day were three separate meetings between the ASEAN leaders and representatives of the United States, China and South Korea.
In deciding to sideline the Myanmar junta boss, ASEAN cited his failure to make steps to end hostilities, initiate dialogue, allow humanitarian support and grant a special envoy full access in the country.
Michael Vatikiotis, Asia Director of the Geneva-based Center for Humanitarian Dialogue, said Myanmar's junta "probably cares about being frozen out of the summit", although it has a history of enduring international isolation.
The National Unity Government is an alliance of pro-democracy groups and ethnic minority armies formed after the coup.