Defence Minister Jose Pedro Aguiar-Branco told reporters the Portuguese jets successfully intercepted, identified and accompanied two Russian aircraft out of the international air space under the Portuguese jurisdiction.
"This means that the system worked again ... The Air Force is ready to carry out these missions every time that the NATO air command requests this," he said.
Local media said the Russian planes involved were two Tupolev Tu-95 strategic bombers and that they flew near the approach path for commercial aircraft to Lisbon international airport.
On Thursday, following a similar incident the previous day, Foreign Minister Rui Machete said the Russian attitude was "not very likeable", but added that its "significance is not worth exaggerating".
On Wednesday, NATO aircraft, including Portuguese, tracked Russian aircraft over the Atlantic, the Black Sea and the Baltic. There has been no violation of NATO air space, but such high numbers of sorties and the fact that the planes are pushing further south are unusual, according to the Western alliance.
NATO has conducted more than 100 intercepts of Russian aircraft so far this year, about three times as many as in 2013, before the confrontation with Moscow over separatist revolts in ex-Soviet Ukraine soured relations.