Instead, the "extremely disappointed" US first lady will return directly to Washington.
"Due to a weather call, the first lady's plane has been grounded in Doha and unable to travel to Amman," an official travelling with Obama said.
"After 36 hours of standing by, the decision was made to return to Washington DC.
"The first lady is extremely disappointed to not be visiting Jordan during her visit to the region."
She is expected to fly home on Friday.
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Obama had originally been due in Jordan on Wednesday afternoon as part of her solo tour to the region.
But storms and flash floods in Amman meant she had been unable to leave Doha after delivering a keynote speech to an education conference in the Qatari capital.
She was on a seven-day visit to the two countries and had arrived in Qatar on Monday.
Her trip came as part of her programme to highlight the plight of millions of girls worldwide who are unable to finish schooling.
In Jordan she had been expected to visit a school in Amman built with US aid funds.
At the conference in Doha, Obama had called for an end to "outdated laws and traditions" which prevent girls completing their education.
She also visited a major US air base in Qatar alongside television chat show host Conan O'Brien.