The fourth seed Indo-Pak pair lost their quarter-final 2-6, 4-6 in just 59 minutes to their Spanish unseeded rivals. Bopanna and Qureshi are world number six in the team rankings at present and need to stay in the top-eight to qualify in the season-ending World Tour Finals in London.
Third seeds Mahesh Bhupathi and Max Mirnyi advanced to the semifinals with a 6-3 6-7(6) 10-6 win over Czech Frantisek Cermak and Slovakia's Michal Mertinak.
Bhupathi and Mirnyi will next face top seeds Lukasz Kubot of Poland and Oliver Marach of Austria in the euro 1,357,000 hard court event.
Bopanna and Qureshi had plenty of chances but could not cash any.
In all, they had seven breakpoints - two in the first set and five in the second - but could convert none.
The Spaniards though converted all three breakpoints they got in the match. They broke Bopanna and Qureshi twice in the opening set and once in the second to book a place in the semifinals.