The Nikkei fell 44.81 points to 11,601.68, after ending Tuesday's session at its highest level since July 2.
The broader TOPIX index lost 0.28 percent to 1,164.94.
"After recent gains in the market, investors were looking for a chance to lock in profits, so some used the GDP outcome as a reason to sell," said Yoshihiko Kosuga, equities general manager at Mizuho Investors Securities.
First-section volume declined to 1.488 billion shares, the smallest daily total since January 27 and down from 1.518 billion on Tuesday. Decliners outnumbered advancers 1,095 to 403.
Honda shed 0.4 percent to 5,540 yen after hitting a five-month closing high on Tuesday. Shares of Sony Corp which hit a one-month high on Tuesday, gave up 0.3 percent to 3,970 yen.
Mitsui Fudosan Co Ltd, Japan's biggest real estate firm, lost 2 percent to 1,315 yen, dragging down the sector subindex by 2.25 percent and making it the worst performing sector.
General contractor Taisei Corp lost 2 percent to 390 yen after it announced plans on Tuesday to raise up to $357 million through a new share issue.
Some analysts welcomed a retreat in the market, however, saying it provided a good buying opportunity.
Toshiba, Japan's second-largest electronics conglomerate, rose together with many of its rivals after the GDP data showed corporate capital spending increased 0.7 percent quarter-on-quarter, bolstered by healthy corporate profits.
Toshiba gained 1.6 percent to 447 yen, the highest level since December 3. Buying in Toshiba was also fuelled after its president told Reuters in an interview that Toshiba's personal computer unit would likely post a higher profit in the next business year than the estimated 6 billion yen ($57.44 million) for the current year, helped by cost cuts.
Tokyo Electron Ltd, the world's second-biggest supplier of semiconductor manufacturing tools after Applied Materials Inc, was up 1.1 percent at 6,540 yen.
These stocks were also helped by gains in shares of Applied Materials in after-hours trading in New York after the company's CEO said he saw an upturn for its products at the end of its fiscal second quarter.
Elsewhere, Miura Co, Japan's leading maker of small industrial boilers including waste-heat boilers, rose 2 percent to 2,030 yen, its highest since June 1991, as the Kyoto Protocol to fight global warming came into force on Wednesday.