But his challenger Nationalist Party leader Lien Chan said on Saturday that he had "suspicions" about the vote and would seek to nullify it.
Final results showed Chen had won re-election to a second four-year term, the Central Election Commission said on Saturday. Chen won by just 30,000 votes.
But Lien says he will challenge the vote results.
“There was not just single but a series of actions that made all of us feel that there were clouds of suspicions,” Lien told a cheering crowd at his campaign headquarters.
A total of about 13 million ballots were cast, the station said.
Lien also mentioned the bizarre assassination attempt on Friday against Chen and his Vice President Annette Lu.
Both leaders survived without life-threatening injuries, but no suspects have been identified.
Taiwan Vice President Annette Lu rejected opposition allegations the presidential election was unfair and said the island's democratic process must be respected.
Taiwan's first islandwide referendum on rival China's military threat and possible talks with Beijing failed to pass on Saturday because of low voter participation, the Central Election Commission said.
The failure of the referendum, which asked Taiwanese whether the island should beef up defences if China refuses to withdraw missiles targeting the territory, was a big blow to President Chen Shui-bian.
He had argued that such a defeat would be a victory for China. The two sides split amid civil war in 1949.
Only 45% of eligible voters participated in the two ballot issues, the commission said. To be valid, the referendum needed at least 50% participation.