Garzon said the PCTV and ANV were co-operating with a "terrorist" organisation, illegally forming a non-terrorist organisation, and suspected of subsidy fraud and possibly embezzlement.
The headquarters and offices of the two parties as well as their websites were ordered closed and their bank accounts frozen.
In Spain, all parties with seats in national, regional or local legislatures receive subsidies.
The suspension did not include seats won by the parties in regional or local elections.
'Stop repression'
A pre-dawn explosion on Friday, blamed on Eta, caused serious damage to a courthouse in the Basque town of Bergara. No one was injured.
Since Batasuna was declared illegal in 2003, Friday's ruling means no pro-independence Basque party will be represented in the Spanish parliamentary vote on March 9.
ANV party members held a news conference in the Basque seaside resort of San Sebastian late on Friday in defiance of Garzon's ban.
About 50 supporters wore T-shirts which read "Free our country. Stop repression," and told journalists they would find a way to be present for the March elections.
The supreme court said on Friday it would not outlaw the parties altogether, although its 16 magistrates, headed by Francisco Jose Hernando, ruled that all public financing of the two parties be stopped, and that the ANV could not take part in March elections, backing up Garzon's decision.
The court banned Batasuna on grounds that it was part of Eta, which has been fighting for an independent Basque state since the late 1960s.
The ban also aimed to cut off Eta funding and propaganda.
To get around it, Batasuna resurrected two little-known parties and had them field pro-independence candidates.
The PCTV party won nine seats in the 75-member Basque regional parliament in 2005.
The ANV party took part in municipal elections last year. Though half of its candidates were barred over alleged links to Batasuna, those remaining won 337 seats in towns and villages in the Basque region, and another 100 in neighbouring Navarra.