Schalke 04 striker Kuranyi bagged his 16th and 17th international goals to give Germany a three-point lead at the top of Group D over second-placed joint rivals the Czech Republic and Ireland following the deserved win in Prague.
The 25-year-old struck on 42 minutes when a well-placed header beat Chelsea goalkeeper Petr Cech and he repeated the feat on 62 minutes when he headed midfielder Bernd Schneider's cross home.
Czech striker Milan Baros managed a consolation goal on 76 minutes after he deflected a shot past Germany's Jens Lehmann which wrong-footed the Arsenal goalkeeper, but it was too little, too late.
"We deserved the win," said Kuranyi. "We kept them under a lot of pressure and the team played well as a unit."
Germany captain and Chelsea midfielder Michael Ballack was pleased with the win as his side face Denmark at home on Wednesday night in a friendly.
"It was a good performance," he said. "We controlled the game in the first half and although it became quite tight after they pulled back a goal, we still deserved the win."
Unbeaten Jogi delighted with win
Unbeaten with seven wins from eight games under his stewardship since taking over from Jürgen Klinsmann after last year's World Cup, Germany coach Joachim Löw was delighted with the three valuable points away from home.
"This was an important and deserved win," he said. "The team played very well and showed plenty of intelligence in their build-up. The defense was rock solid and we barely gave the opposition any chances, so we have to be very happy. It was very important to go 2-0 up to give us a cushion, Kevin (Kuranyi) was highly motivated and had a superb game."
Germany created the best chances throughout with Ballack linking well with midfield partner Bastian Schweinsteiger which tested the home side's defense in the early stages.
German midfield key to victory
Ballack created the best chance in the opening 20 minutes when his free-kick was charged down, but he managed to chip over the defense and Schweinsteiger failed to connect with the ball.
And Bayern Munich's Lukas Podolski, voted Best Young Player of last year's World Cup, forced Cech into a good diving save after he connected with a powerful shot on 25 minutes.
The threatened breakthrough finally came in the 42nd minute when Kuranyi rose above his marker and headed the ball just inside the post. Podolski hit the crossbar moments later.
The hosts pushed hard for an equalizer after the interval and the best chance fell to Tomas Rosicky, who hit his volley with some force into the waiting arms of Arsenal team-mate Lehmann on 55 minutes.
But Kuranyi made sure of the win for Germany when he slipped his marker and met Schneider's cross to claim his second goal of the game just after the hour mark.
Baros gave the Czechs some hope when he deflected Jan Polak's long-range shot past Lehmann on 76 minutes as the home side piled on the pressure in the closing stages, but it was not enough to threaten the result.