They are accused of taking part in killings and disappearances of dozens of leftists and opposition activists during the so-called "dirty war" waged under Pinochet's rule over Chile between 1973 and 1990.
The identities of those named in the warrants issued on Tuesday were not released.
Ordering the arrests Judge Victor Montiglio said the 129 were members of the army, air force and uniformed police who worked for the Dina.
Their alleged crimes were said to have been committed as part of Operation Condor, the Colombo Operation and the Street Conference, campaigns which targeted opponents of military regimes in Chile and other South American nations.
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| Pinochet died in December 2006 evading attempts to prosecute him [AP] |
"We are investigating all who have participated ... in the deprivation of liberties of the victims," Montiglio said.
"We are much nearer the end" of the process, he added.
Pinochet led a military junta that seized power in 1973, overthrowing Chile's elected Marxist President Salvador Allende in 1973 and launched a brutal campaign to root out leftist supporters.
According to a government report, at least 3,197 suspected leftists were killed for political reasons before he left power in 1990.
Many of the victims vanished, believed to have been kidnapped, killed and buried in unmarked graves, leaving relatives with no word on their fate.
Pinochet himself died in December 2006, evading several attempts in Chile and abroad to prosecute him for human rights abuses.