Kerzhakov's smart finish made it three wins from three at the start of Russia's Group F campaign, while defeat for Portugal ends their 100 per cent start and leaves them trailing Fabio Capello's men by three points.
Russia will fancy their chances of maintaining their perfect start when they play host to Azerbaijan on Tuesday, while on the same night Portugal will bid to get back to winning ways when they welcome Northern Ireland.
Just six minutes were on the clock when the home side went ahead at the Luzhniki Stadium tonight.
Roman Shirokov was the architect as he ran on to a pass from Viktor Faitzulin and delivered a superb first-time through-ball that Kerzhakov collected before lifting his finish over the advancing Rui Patricio.
The early goal sparked an immediate response from the visitors, with Cristiano Ronaldo forcing a good save from Igor Akinfeev in the 10th minute before Helder Postiga headed over from the resulting corner.
With 14 minutes gone Portugal attacked again, this time Bruno Alves turning a powerful header on target from a Miguel Veloso free-kick but Akinfeev was again on hand to make the save.
Despite that brief spell of pressure Portugal were unable to create any clear-cut chances for the remainder of the first period, and as the second half went on their frustration increased.
The mood of the Portuguese camp was not improved when Ronaldo went down clutching his face following an off-the-ball tangle with Aleksandr Aniukov on the edge of the Russian box just before the hour.
Referee Viktor Kassai was unimpressed with the Real Madrid man's typically theatrical reaction to the contact and waved Ronaldo to his feet.
Akinfeev kept Russia's lead intact with another save from a Postiga in the 63rd minute, while a short time later Ronaldo blazed an effort over the bar from the edge of the box.
Although Portugal needed to find a goal it was the hosts who finished on the front foot, with Shirokov going close to adding a second in the 73rd minute when he fired a low shot at Patricio.
And with 82 minutes gone Portugal we indebted to Patricio for keeping the deficit at one goal as he pulled off a superb parry from Aleksandr Kokorin's fierce effort from the edge of the box.