"Malaysian authorities devoted considerable manpower and resources to the search-and-rescue (SAR) operations," the Singaporean premier said in his Facebook post, according to Bernama news agency.
The two hikers, Dominick Tan and Clarice Lum Jie, were reported missing in the Gunung Pulai Forest Reserve, Kulai, since Monday (Feb 5). They were found safe at the Ulu Choh Dam in Pontian on Wednesday (Feb 7).
"My heartfelt thanks to Johor police chief Datuk Mohd Khalil, Kulai Fire Department Chief Mohd Khairi Zainudin, their teams, as well as the Singapore team on the ground, for their efforts in this operation.
Lee said he was "relieved" that the duo have been found.
"The pair were eventually spotted by a rescue helicopter this morning (Wednesday), picked up by a rescue boat, and are now on their way back home," wrote Lee.
Dominick and Clarice, both 27, were found by the SAR team at 11.24am, about 50km from the last location they were detected following a distress call received via 999 on Monday.
The climbers had reportedly entered the Gunung Pulai area at 12.15pm on Monday and made a distress call to the authorities at 5.55pm on the same day. They were last contacted at about 10pm.
The pair were spotted at a lake near the dam via an aerial reconnaissance using a Royal Malaysia Police Force helicopter.