Somdev, ranked 113th in the world, will now take on Great Britain's James Ward in the Round of 32, in a bid to seal a spot in the main men's singles event.
Somdev Devvarman will next face American Robby Ginepri, ranked 123 places below him at 236.
The Russian, who won the French Open on clay last year, brought a 16-match winning streak on the surface into Madrid and was strongly favoured to coast past a player who has been dogged by knee injuries.
Robby Ginepri became the first American to win his way into the second round of the BNP Paribas Open by beating Paoli Lorenzi of Italy 1-6, 6-3, 6-4 on Thursday.
Fourth-seeded Alexandra Dulgheru of Romania and No. 7-seeded Mathilde Johansson of France were knocked out in the first round of the Monterrery Open on Tuesday.
Alexandra Dulgheru became the latest seed to exit the Barcelona Open when she was beaten 7-5, 6-3 by Spanish qualifier Estrella Cabeza Candela on Wednesday.