There were no reports on Monday of deaths or serious injuries from storm, which headed for the Gulf of Mexico.
"The worst is over," Felix Gonzalez, governor of Quintana Roo state, which includes Playa del Carmen and the resort city of Cancun, told Mexico's Televisa television network.
Thousands of residents and foreign tourists spent the night in improvised shelters set up in hotels along the famous Mayan Riviera coastline, on the eastern side of the peninsula.
The storm's wind speeds had soared to as much as 215 kph, making it a fierce Category Four storm when it hit Mexico.
It had weakened to Category Two as it passed over the Yucatan Peninsula early on Monday with maximum sustained winds of 160 kph.
The storm was expected to emerge into the gulf, possibly regaining strength, later on Monday.
Its centre roared ashore near Tulum, a collection of thatched-hut lodgings alongside ancient Mayan ruins 160km south of Cancun.
Damage from Emily was evident everywhere on the Mayan Riviera, whose white-sand beaches and turquoise waters attract Mexican and foreign tourists.
Damage was evident everywhere
on the hurricane's path
Power was knocked out all along the coast.
The force of the hurricane's winds snapped concrete utility poles in two along a kilometre stretch of highway between Playa del Carmen and Cancun to the north.
Plate-glass windows were shattered on the ground floors of businesses in Playa del Carmen, while residents waded through knee-deep water along streets.
On Sunday in Cancun, hundreds of buses moved more than 25,000 people, mostly tourists, to temporary shelters, evacuating them from hotels and low-lying seaside neighbourhoods that were battered by strong waves.
About 60,000 tourists were evacuated all together from Cancun, Tulum, Playa de Carmen and Cozumel, an island just south of Cancun famous for its diving.