"We have played a very good match, on high speed and with great desire," Russia coach Fabio Capello said. "We've reached our goal."
Portugal, a 2012 European Championship semifinalist, failed to impress against Israel in what has been a lackluster qualifying campaign, with Cristiano Ronaldo producing a muted performance in the Portuguese capital.
A blunder by goalkeeper Rui Patricio cost Portugal victory as his 85th-minute clearance went straight to Ben Basat, who canceled out Ricardo Costa's 27th-minute strike.
The game was tense to the end as a below-par Portuguese team held onto its slender lead.
Portugal's qualification bid went off track earlier in the campaign with a 1-1 home draw against Northern Ireland and a 3-3- draw in Israel, and Friday's lukewarm match was reminiscent of those displays.
The Portuguese defense was depleted by the absence of three regular starters, but its attack was the weakest point and the team struggled to find its rhythm going forward.