In the brief telephonic conversation, Obama condoled the loss of lives, the Prime Minister's Office said.
"The two leaders took the opportunity to review developments in Indo-US relations," it said.
The Obama administration has offered FBI help in the investigation into Saturday's blast at the German Bakery, a popular eatery in Pune's posh Koregaon Park area.
The US State Department has said it is working with India and Pakistan to combat the threats the three countries face from terrorist and extremist groups.
"The information we have shared so far has been quite unprecedented, and we intend to continue to working with the Government of India to try and protect our two societies from these types of attacks," Acting US State Department Spokesman Gordon Duguid said.
Photograph: White house Photos