Addressing the opening of the UN General Assembly, Guterres said he "took note" of Suu Kyi's pledge to abide by the recommendations of a report by former UN chief Kofi Annan that has advocated citizenship for the Rohingyas.
"But let me be clear," Guterres said. "The authorities in Myanmar must end the military operations, and allow unhindered humanitarian access."
More than 420,000 Rohingya have been forced to flee violence in Myanmar's northern Rakhine state in what the United Nations has described as "ethnic cleansing."
In her nationwide address, Suu Kyi insisted that army "clearance operations" in response to attacks by Rohingya militants had finished on September 5 and denied that Rakhine was in flames.
"More than 50 percent of the villages of Muslims are intact," she said.
The Nobel laureate called for patience and understanding of the unfurling crisis in her "fragile democracy" and pledged to resettle some refugees, but she did not speak out against the military campaign.
"We are all shocked by the dramatic escalation of sectarian tensions in Myanmar's Rakhine state," Guterres told world leaders.
In an interview earlier this week, Guterres described the address by Suu Kyi as "a last chance" to speak out and put in motion an end to the mass exodus.
The 1.1-million strong Rohingya have suffered years of discrimination in Myanmar, where they are denied citizenship even though many have longstanding roots in the country.
Myanmar's second Vice President, Henry van Thio, is to take the podium at the assembly on Wednesday after Suu Kyi decided against attending this year's world gathering.