The 27th seed tried his best to make a comeback into the match but eventually lost 3-6, 6-7(4) to his Slovenian opponent, ranked 126 in the ATP chart.
Somdev had last year qualified for the US Open and reached the second round of the singles main draw.
In Saturday's two hour 22 minutes contest, Somdev broke his rival thrice including twice in the second set and dropped his serve twice in each set.
Yuki Bhambri and Prakash Amritraj had also made it to the singles qualifying draw but lost in the first and second round respectively.
Yet again, Sania Mirza will India's lone challenge in the singles when she competes in the women's main draw.