Spain raised € 3.2 billion ($4.1 billion), within the range it had targeted but below the maximum €3.5 billion it had sought.
Demand was just 1.5 times the amount offered, less than at previous similar auctions.
The Treasury sold €2.15 billion of 10-year bonds and €1.05 billion of 15-year bonds.
Yields on the ten-year bond rose to 2.196 per cent, up from 2.075 per cent during the last similar auction in October when it hit a historic low.
Ten-year bonds are considered to be the main barometer of a country's standing on the eurozone bond market.
Yields on the 15-year bond fell to 2.842 per cent, down from 3.514 per cent during the last similar auction in May.
Spain, the eurozone's fourth-largest economy which exited recession last year, plans to borrow slightly over €242 billion from debt markets this year, with €133 billion in medium- and long-term bonds.
Investor sentiment for Spain, which came close to requesting a sovereign bailout at the height of the eurozone crisis, had improved in previous auctions due to its better growth outlook and growing confidence in eurozone periphery countries.
But lower growth forecasts in Germany, the eurozone's largest economy, and ultralow inflation, have fulled fears over slowing global growth and hurt sentiment for eurozone periphery nations.
Bond yields for these countries shot up on Thursday in the secondary trading markets, indicating that investors are demanding more to hold on to debt from these countries.
The yield on Spanish 10-year bonds jumped to 2.356 per cent from 2.116 per cent on Wednesday.
Greek 10-year bonds jumped to 8.656 per cent from 7.854 per cent. Portugal rose from 3.585 per cent from 3.286 per cent, while Italy climbed to 2.665 per cent from 2.422 per cent.
European stock markets also slumped following the Spanish bond auction, with the Paris, Milan, Madrid, Lisbon and Amsterdam exchanges each fell by more than 3 per cent.