The decree, signed by President Vladimir Putin, was described by Moscow as "temporary" until a "political solution" is found to bring peace to the region.
"Identity papers, school or professional diplomas, birth and death certificates, ... Issued by the competent bodies in the zones mentioned are recognised as valid by Russia," read the decree.
It listed the territories concerned as the self-declared Lugansk People's Republic (LNR) and the Donetsk People's Republic (DNR).
Both Ukraine and the West -- which has imposed sanctions on Russia as a result of the unrest -- say the separatist regions receive humanitarian and military backing from Moscow, although Russia has not until now officially recognised them.
The document adds the measures are "temporary, (lasting) until the situation in the Donetsk and Lugansk regions find a political solution based on the Minsk accords" signed in February 2015 and designed to bring a truce to the region.
Kiev immediately condemned Putin's decree.
"It's a deliberate provocation by Putin," Ganna Gopko, head of the foreign affairs committee of the Ukrainian parliament told AFP.
"It amounts to a genuine legalisation by the Kremlin of Donbass," another name given to the parts of eastern Ukraine controlled by pro-Russian rebels, she said, adding that the decree proved that Putin was seeking "an escalation" of the situation.
The war has cost cost some 10,000 lives since Ukraine's mostly Russian-speaking eastern industrial regions revolted against Kiev's pro-Western government, after the ouster of the former Soviet republic's Kremlin-backed president.
"We are very grateful to Russia for this gesture," Interfax news agency quoted Denis Puchilin, a DNR leader, as saying.
Authorities in pro-Russian rebel held areas last March began distributing passports very similar to Russian ones bearing a two-headed eagle on a red backdrop.
Earlier this month, Kremlin spokesman Dmitri Peskov insisted that Moscow would recognise papers issued by the separatist authorities "only for humanitarian reasons," and even then, only in exceptional cases.
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