The designation issued on Friday requires Meduza to label itself as such, subjecting it to increased government scrutiny.
"We reject the decision by the Russian authorities to include independent media outlet Meduza on the list of 'foreign agents'," a spokesman for EU foreign policy chief Josep Borrell, said in a statement.
This is the third contract sealed by the bloc with the two companies, which have already agreed to deliver 600 million doses under two previous contracts.
Dubbed "blank check" companies in the United States, SPACs have attracted billions of dollars in investment on Wall Street and their popularity has spilled over into Europe.
Nevertheless there was some good news as BioNTech/Pfizer announced that 50 million doses that were due to arrive in Europe in late 2021 will instead start arriving as early as this month.
The EU-UK trade pact was provisionally applied on January 1, after nine months of tough negotiations and a last minute handshake just before Christmas last year.
Erdogan has downplayed EU membership in recent years as the bloc has ramped up criticism of Ankara's foreign policy and rights record, and dangled the threat of EU sanctions.
EU spokesman said the reported incident "could have been an act of sabotage" but insisted that there had been no official attribution over who was responsible.
Northern Irish justice minister Naomi Long, of the centrist Alliance Party, noted that Johnson and Lewis "denied the existence of borders, even as those borders were being erected".