Mr Xi had been waiting for a sign from Washington before he send his best wishes, treading a diplomatic tightrope between appeasing Donald Trump and getting off to a smooth start with Mr Biden.
Russia and Mexico are now the only major world powers yet to congratulate Mr Biden.
Four years ago, the Russian leader Vladimir Putin was among the first to congratulate Mr Trump on his election victory, but there has been no tweet, telegram or phone call to Mr Biden this time.
The Chinese leader expressed hope the two countries could promote the healthy and stable development of bilateral relations, the official Xinhua news agency reported.
Also on Wednesday, Chinese Vice President Wang Qishan congratulated Mr Biden's running mate, Kamala Harris, on being elected the next US vice president, Xinhua said.
China’s foreign ministry spokesman issued a statement on 13 November wishing Mr Biden well, but Mr Xi’s refusal to congratulate Mr Biden was noted.
"We respect the choice of the American people. We extend congratulations to Mr Biden and Ms Harris," the foreign ministry spokesman said.
The decision on Monday by the General Services Administration head, Emily Murphy, to unlock $9 million in transition funds and allow Mr Biden’s team access to government officials appears to have influenced Beijing’s decision.
Mr Trump is rapidly running out of legal avenues to pursue, and White House reporters say that even the president himself has come to the conclusion that it is futile to fight on.
He has shown no sign of conceding, however.
On Wednesday he is intending to hold a press conference in Gettysburg with his lawyer, Rudy Giuliani, who is spearheading efforts to overturn the vote.
Whether he actually concedes is irrelevant.
On 14 December the electors will meet to cast their votes, and the person who received the most - Joe Biden - will be inaugurated on 20 January.