The meeting added to global pressure on Suu Kyi to take action to end the crisis for the Muslim minority, with US Secretary of State Rex Tillerson due Tuesday also to hold talks with her in Manila then travel to Myanmar.
"The Secretary-General highlighted that strengthened efforts to ensure humanitarian access, safe, dignified, voluntary and sustained returns, as well as true reconciliation between communities, would be essential," a UN statement said, summarising comments to Suu Kyi.
The crisis erupted after Rohingya rebels attacked police posts in Myanmar's Rakhine state, triggering a military crackdown that saw hundreds of villages reduced to ashes and sparked a massive exodus.
Authorities have blocked independent access to northern Rakhine.
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But journalists and UN officials have collected reams of testimony from Rohingya refugees in Bangladesh describing soldiers and Buddhist mobs committing murder, rape and mass arson.
Following its first official investigation into the crisis, the army published a report this week in which it cleared itself of any abuses.
But she lacks control over the powerful military, which ruled the country for decades until her party came to power following 2015 elections.
The United States has been careful not to place blame on her and has focused instead on the army's role in the conflict.
Guterres and Suu Kyi met in the early hours of Tuesday morning, according to his office.
In a summit on Monday night with leaders of the 10-member Association of Southeast Asian Nations, of which Myanmar is a member, Guterres also voiced concern about the Rohingya.
He described the situation as a potential source of instability in the region, as well as radicalisation.