Last year's record flight lasted for 32 days, five hours and 51 minutes.
Nasa hoped the helium-filled balloon would remain aloft for 100 days or more.
The balloon and its Compton spectrometer and imager payload were brought down in Peru on Saturday afternoon.
Nasa balloon programme office chief Debbie Fairbrother explained yesterday the decision to conclude the mission came after the balloon operators noticed altitude variations during the last few weeks of the flight over the Pacific Ocean.
At night, the balloon dropped as much as 12km from its optimum altitude of 33km as it flew over -80degC storms, and would then return to 33km at sunrise.
Ms Fairbrother said the altitude variation could have occurred if some of the balloon's helium "bled off'' during one of the initial, harsher cold storms.
Having identified a safe landing area over the southern tip of Peru, "flight termination commands'' were sent to the balloon, she said.
The 532,000cu m balloon then separated from the payload and rapidly deflated, and the payload floated safely to the ground, touching down in a mountainous area about 30km north of Camana, Peru.
Recovery of the payload and balloon was in progress, she said.
The overall flight duration record for a super pressure balloon is 55 days.
