Eyewitnesses said the monks protested for about an hour before dispersing.
Marches against military rule over the past five days have attracted thousands of young monks to the streets of Yangon and other cities including Mandalay.
A month of protests, begun by civilians against economic hardship and fuel-price increases, has now grown into the biggest grass-roots political movement in two decades.
On Saturday, the army allowed about 2,000 monks and civilians to pass a roadblock and gather by Aung San Suu Kyi's lakeside home on University Avenue.
She greeted them from the house where she has been detained for 12 of the past 18 years.
"I think all the people of Myanmar must act to get democracy for a better life"
aprat_1992, Denpasar, Indonesia
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Witnesses said Aung San Suu Kyi was in tears as she greeted the cinnamon-robed monks.
The 62-year-old Nobel Peace prize winner has become an internationally recognised figurehead of Myanmar's pro-democracy movement.
They were chanting for around five minutes before she and two other women stepped out of a side door of her home, one witness said.
Unable to hold back her tears, Aung San Suu Kyi waved to the monks and their supporters as they paused outside the gates to chant prayers for peace.
The monks spent about 15 minutes chanting the same Buddhist prayer they had recited through much of their earlier march in Yangon, the witnesses said.
"May we be completely free from all danger, may we be completely free from all grief, may we be completely free from poverty, may we have peace in heart and mind," they intoned.
Some of their supporters broke into tears as they joined in with their own refrain, chanting in turn: "Long life and health for Aung San Suu Kyi, may she have freedom soon."
The military often posts armed guards to block traffic on University Avenue to prevent traffic from passing by, but witnesses said the monks had persuaded the 20 armed guards to raise the blockade.
"They told the guards that they just wanted to go to pray for Aung San Suu Kyi, because we are Buddhists," one witness said.
The guards did not interrupt the monks during their prayers, but closed the roadblock after they left.
The gates to her compound stayed shut throughout, but one witness said that at one point, Aung San Suu Kyi was only five feet away from the monks.
Monks are rumoured to be planning another march at midday, while one underground group has called for nationwide prayer vigils to begin.
For their part, Myanmar's military rulers have refused to tell citizens about the protests, choosing instead to fill its state-run newspaper with reports of floods and traffic.
|Monks have marched in rains to keep up|
their protest in Myanmarese cities [AFP]
There were no reports on Sunday of the monks' protests.
The state-run New Light of Myanmar
prominently featured a story about General Than Shwe, the government head, sending greetings to Saudi Arabia on its national day.
Inside, there were stories on floods, paddy plantings and efforts to prevent river erosion.
The newspaper derided the National League for Democracy led by Aung San Suu Kyi as "incompetent and seeking political gain".
The NLD won elections in 1990 by a landslide, but the Myanmarese military never recognised the result.