Germany remain a point clear at the top of Group Four on seven points with two wins and a draw after their win over Guus Hiddink's Russia team who are fourth in the table with three points from last month's 2-1 win over Wales.
Podolski and captain Ballack scored within the first half hour to give the home side a 2-0 lead at the break. But Russian play-maker Andrei Arshavin scored early in the second-half and the guests had Germany under pressure right up to the final whistle.
"We played well in the first-half and grabbed two nice goals," said Ballack, who missed Germany's last two games with injury. "But the Russians didn't allow us any peace and so nearly earned a goal right up until the end."
Podolski finds it easier to get into the Germany team than the Bayern side having spent most of the season on the bench and the 23-year-old now has 31 goals in 58 internationals. "The coach gave me the chance again and I paid the confidence back with a good game," said Podolski.
"That was one of our best performances, but the Russians had us under intense pressure in the second-half."
Injuries meant striker Roman Pavlyuchenko, defender Denis Kolodin and midfielder Dmitry Torbinsky were all missing from Hiddink's selection. The only surprise in Joachim Löw's Germany team was the midfield inclusion of Stuttgart's Thomas Hitzlsperger for fit-again Torsten Frings, who along with Ballack, missed last month's 6-0 win in Liechtenstein and the 3-3 draw in Helsinki through injury.
A broken hand suffered by first-choice goalkeeper Robert Enke on Wednesday gave Bayer Leverkusen's 23-year-old Rene Adler his debut in goal for Germany. He was tested early on when Yuri Zhirkov got in behind the German defence and put in a cross which lone striker Pavel Pogrebnyak just failed to convert inside the first five minutes.
German defender Philipp Lahm and Ballack both went close moments later as the home side increased the pressure. Germany took the lead when striker Miroslav Klose slipped the ball through the defence and Podolski turned his marker before making sure he was the first to the ball in the penalty area to fire home on nine minutes.
And the home side went 2-0 ahead when Bastian Schweinsteiger's pass put his captain Ballack into the penalty area and the Chelsea star volleyed home from five metres out on 28 minutes. It was so nearly 3-0 when Podolski rifled his shot home on 33 minutes, but Akinfeev pushed the ball around the post to make it 2-0 at the break.
Russia's attack - which so impressed during Euro 2008 when they reached the semi-finals - finally made an impact on 51 minutes when Zenit St Petersburg midfielder Arshavin stabbed home his shot with Adler under intense pressure.
Germany were soon back on the attack and ex-Aston Villa midfielder Hitzlsperger went close with a long-range volley approaching the hour mark and Hamburg winger Piotr Trochowski beat Akinfeev, but hit the bar moments later. Russia should have equalised when a ball over the defence put Progrebnyak one-on-one with Adler, but the German keeper scrambled away the danger.
Adler was repeatedly tested in the dying minutes, but Germany held their lead to take the three points.
In the next round of Group Four games, Germany face Wales at home in Mönchengladbach on Wednesday, the same night Russia play Finland in Moscow.