(updates with 50 pct of ballots counted)
Challenger Alejandro Garcia Padilla was clinging to a lead of less than 4,000 votes over incumbent Puerto Rican Gov. Luis Fortuño with 50 percent of the ballots counted, the State Elections Commission said late Tuesday.
The candidate of the PPD had an advantage of 47.71 percent to 47.29 percent over the governor, who heads the PNP.
Juan Delmau, standard-bearer of the small Puerto Rican Independence Party, stood at 2.52 percent, while three other minor-party hopefuls were hovering around 1 percent, the commission said.
Neither Garcia Padilla nor Fortuño have commented on the results, but PPD sources said they were confident of victory based on the party's internal polling.
In the other major race, for the post of non-voting representative to the U.S. Congress, PNP incumbent Pedro Pierluisi was beating the PPD's Rafael Cox Alomar by 48.43 percent to 41.12 percent.
Tuesday's ballot also included a non-binding referendum on the future of Puerto Rico's relationship with the United States. The vote was running 53 percent to 46.9 percent in favor of ending the island's current commonwealth status.
The PNP favors U.S. statehood for Puerto Rico, while the PPD advocates an enhanced commonwealth status.
More than 2.4 million people were eligible to cast ballots on Tuesday.
Besides the race for governor and resident commissioner in Washington, voters chose the 78 members of the Puerto Rican legislature and the mayors of the island's 79 municipalities.