It was one rubber in which India entered as favourites but the fancied team were tamed by the Czechs 5-7 2-6 2-6 in two hours and 10 minutes.
It was Paes' only second defeat in a Davis Cup doubles in the last 15 years. The last defeat had also come with Bopanna against Uzbekistan in an away tie in 2012.
It was also the first defeat for Paes in a home tie since 2000 when he and Syed Fazluddin had lost to Lebanon's Ali Hamdeh and Jicham Zaatini in Lucknow.
The result leaves Somdev Devvarman and Yuki Bhambri with a daunting task of winning both the reverse singles tomorrow if India are to re-enter the elite 16-nation World Group.
Yuki will take on left-hander Jiri Vesley in the fourth rubber while Somdev will clash with big-hitting Lukas Rosol in the fifth match.
Bopanna, world number 13 in doubles rankings, was rusty today as he lacked control over his shots and there was no sting in his serve either.
On the other hand, Adam packed a lot of punch in his shots with impressive hand and eye co-ordination. His returns were solid and at net too he was a delight to watch. He hardly missed a shot and was a winner in his duels with both Paes and Bopanna.
In each set, Indians were first to lose serve and the Czech took full advantage of their lead.
