Alex Oxlade-Chamberlain also scored for the hosts, who moved to the top of Group H.
It wasn't such a good night for Oxlade-Chamberlain's Arsenal teammate, Theo Walcott, who will spend the night in a hospital after colliding with goalkeeper Aldo Junior Simoncini early in the game.
Russia's winner against Portugal came with its only shot on goal in the first half, Alexander Kerzhakov scoring in the sixth minute.
Ronaldo, who has scored six times in his last three Spanish league games for Real Madrid, barely had a sniff in Moscow.
"Maybe we weren't as calm as we usually are," said Portugal coach Paulo Bento, whose team is the only leading European nation not to be atop its group at this stage.
Eddie Johnson scored two goals for the United States, including the winner in second-half injury time, in a 2-1 victory over Antigua and Barbuda. The road win put the Americans in position to advance to CONCACAF's final qualifying round if they draw with Guatemala on Tuesday night in Kansas City, Kan.
Guatemala beat Jamaica 2-1 on Friday night.
In Group B, Mexico was held scoreless for more than 75 minutes by Guyana, but wound up winning 5-0 to stay perfect. Costa Rica held onto second place in the group by winning 1-0 at El Salvador.
Canada beat undermanned Cuba 3-0 in Group C. The Cubans had only 11 players for the game, and finished with 10 after striker Roberto Linares was ejected for a challenge that crumpled captain Kevin McKenna. Four players left the team in Toronto.
In the other Group C game, Honduras and Panama tied 0-0.
In South American qualifying, host Argentina took the overall lead with 17 points as Lionel Messi scored two second-half goals and Sergio Aguero added another. Messi scored in the 66th and added another with a free kick in the 80th while Aguero scored in the 75th.
Alejandro Chumacero scored in the second half to lift host Bolivia into a 1-1 draw with Peru, while Colombia beat Paraguay 2-0.
Radamel Falcao scored two second-half goals as Colombia improved to 16 points in eight matches — among the leaders in qualifying — and left Paraguay with only four points from five matches, the worst record among the nine teams.
Felipe Caicedo scored twice as Ecuador defeated Chile 3-1 in Quito. Ecuador improved to 16 points, Chile has 12.