Milosevic backers conceded defeat earlier in the week in the third race - elections for municipal governments in Serbia.
The parliamentary vote has not generated the same degree of controversy.
According to the commission, pro-Milosevic parties won 74 of the 138 seats in the parliament's lower house, while the opposition bloc received 55 seats. The other seats went to independent parties.
Coalition
In the upper house - where 40 seats are divided equally between the two Yugoslav republics, Serbia and Montenegro - the pro-Milosevic parties had 27 seats, and the opposition 10, with the other seats going to independent parties.
Milosevic backers conceded defeat earlier in the week in the third race - elections for municipal governments in Serbia.
Mr Milosevic's Socialist Party and a coalition of allies had already claimed victory before the results were announced.
A statement from the Serbian Socialist Party, SPS, said it had captured "an absolute majority in the federal parliament" in coalition with the neo-communist Yugoslav Left, headed by Mr Milosevic's wife, and the pro-Belgrade Montenegrin Socialist People's Party.
However, the combined total for the three parties falls short of the two-thirds majority it would need to change the constitution, or vote down a future Yugoslav president.
Municipal results
Analysts also say that the Montenegrin party's loyalty to the two parties in Belgrade could be in doubt due to reports of internal rifts.
The Federal Electoral Commission has not issued any results for municipal elections in Serbia, but Socialist Party officials have acknowledged they had a poor showing at local level.
The main opposition alliance, Democratic Opposition of Serbia (DOS), won 105 out of the 110 seats on the Belgrade city council, virtually wiping out Mr Milosevic's Socialist Party, according to preliminary results.
The DOS won councils in almost every major town.
Vuk Draskovic's Serbian Renewal Party lost all the towns it used to control, including Belgrade, where it did not win a single seat in the city council.
Mr Draskovic offered his resignation to his party on Tuesday.
Vojislav Seselj's Radical party, SRS, also did badly, winning only one seat in Belgrade.