The demonstrators forced their way past riot police after an earlier attempt on Friday was quickly quelled when several windows were smashed.
Some protesters made it to the tenth floor of the building, the home of the Central Election Commission (CEC), but police blocked them from getting into its offices, according to local television reports.
Most of the demonstrators remained in the lobby where they waved national flags and those of the opposition Kuomintang (KMT) chanting "A-bian (Chen's nickname) step down" and "Down with the CEC. Long live the Republic of China" which is Taiwan's official name.
Many more remained outside as the situation calmed and police stood back to allow the demonstration to continue in the lobby.
The break-in came soon after opposition legislator Lee Ching-hua, of the People First Party (PFP) told the crowd that the CEC had confirmed it would name Chen the winner, after leading a small delegation to see the CEC.
Protesters are demanding Chen
(R) resign from office
Protests have continued since Chen beat his sole rival Lien Chan, leader of the KMT, last Saturday by just 0.22% with the opposition blaming an unsolved assassination attempt on the president on the eve of polling and vote-rigging for its loss.
Hundreds of demonstrators shouting "A-bian (Chen's nickname) cheated" and "Election invalid" had gathered hours ahead of the official announcement that is required by law within seven days of an election victory.
One man, speaking to the crowd from the top of an opposition campaign van before the break-in, said: "Let us put aside our tenderness and let us fight."
The windows of a bulletin board outside the building were also smashed and opposition lawmakers urged the crowd to surround it so a notice could not be put up declaring Chen's win.
Election officials said the vote had been fairly carried out and was free of irregularities.
Chiu Yi, another PFP legislator, told the crowd he had spoken with the head of the CEC Huang Shih-cheng.
"We have already told Huang that there are consequences of announcing Chen the winner. If he continues to do that we will never let him get away with it."