Taiwan's High Court ordered that 330,000 ballot boxes across the island be sealed but, as of late yesterday, had not called for the recount demanded by opposition leader Lien Chan.
The Central Election Commission said Mr Chen and Ms Lu had won 50.11 per cent of the vote, just over 29,000 votes more than Mr Lien and running mate James Soong with 49.89 per cent.
Opposition candidates refused to concede defeat on election night, instead angrily raising suspicions over a large number of invalid ballots and the apparent assassination attempt.
Mr Soong said there were "clouds of suspicion" surrounding the result.
Mr Lien said it was "unfair" and demanded a full investigation of the shooting. "Prepare to annul the election," Mr Lien shouted to an angry crowd, many of whom then surrounded the High Court, where leaders of the opposition Kuomintang party went to lodge their lawsuit yesterday.
A referendum held at the same time as the presidential poll – asking voters whether Taiwan should boost missile defences against China and seek peace talks with Beijing – failed because fewer than half the voters participated.
China had condemned the referendum, which it saw as a first step towards a declaration of independence.
Beijing, which considers Taiwan part of "one China", said the failure of the referendum proved it was an "illegal act (which) goes against the will of the people".
The US State Department said in a statement that it was "confident both sides and their supporters will remain calm and will use the established legal mechanisms to resolve any questions about the election results".
The opposition was stunned by the defeat, having expected before the shooting to win easily.
While Mr Chen called the result a "victory for the Taiwanese people", opposition campaign official Su Chi said "the gunshots looked fishy".
Even a key adviser to Mr Chen admitted the incident played a role in the equivocal victory. "We won a considerable sympathy vote. That is the bullet that ended the KMT hope of coming back. That was a blessing in disguise and that was God's will," said Taiwanese legislator Parris Chang. Violent scuffles broke out in Taiwan's second and third-largest cities on Saturday night as opposition protesters surrounded court buildings, broke windows and pushed over barricades.
As the political crisis deepened late yesterday, Mr Chen's office released photographs of the President being treated for a stomach wound in an attempt to quell speculation over whether the shooting had happened at all.
Mr Chen's stomach was grazed and Ms Lu's knee was nicked, apparently by separate bullets, as they campaigned in an open-top jeep through Mr Chen's home town in southern Taiwan. No one has been arrested and police have released few details.
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