The world's busiest air hub for international passengers confirmed a halt to arrivals at 7:26 pm (1526 GMT) before announcing a "gradual resumption" more than two hours later.
Earlier the airport, which had been expecting more than 100 flight arrivals on Tuesday evening, took the equally unusual step of briefly halting its operations in the chaos caused by the storm.
Dubai, the Middle East's financial centre, has been paralysed by the torrential rain that caused floods across the UAE and Bahrain and left 18 dead in Oman on Sunday and Monday.
Dubai airport operations were suspended for 25 minutes in the afternoon before resuming. Unconfirmed images on social media showed planes taxiing across an apron flooded with standing water.
Departure flights remained in operation during the evening but were plagued with delays and cancellations. Access roads to the airport were also badly flooded.
Similar scenes were repeated across Dubai and elsewhere in the UAE as the oil-rich Gulf state, better known for its arid climate and intense summer heat, reeled from the storm.
Both the Oman and the UAE, which hosted last year's COP28 UN climate talks, have previously warned that global warming is likely to lead to more flooding.
Friederike Otto, a leader in the field of assessing the role of climate change on specific extreme weather events, said it was likely that global warming played a part.
"It is highly likely that the deadly and destructive rain in Oman and Dubai was made heavier by human-caused climate change," said Otto, of the Grantham Institute for Climate Change at Imperial College London.
Rain 'scares me'
Flagship shopping centres Dubai Mall and Mall of the Emirates both suffered flooding and water was ankle-deep in at least one Dubai Metro station, according to images posted on social media.
Some roads collapsed, residential communities were hit by heavy flooding and many householders reported leaks from roofs, doors and windows.
Schools were shut across the UAE and were expected to remain closed on Wednesday when further storms are forecast. Dubai's government also extended remote working for its employees into Wednesday.
Some inland areas of the UAE recorded more than 80 millimetres (3.2 inches) of rain over 24 hours to 8:00 am, approaching the annual average of about 100mm.
The National Center for Meteorology "urged residents to take all the precautions... and to stay away from areas of flooding and water accumulation" in a post on X, formerly Twitter.
The Asian Champions League football semi-final between the UAE's Al Ain and Saudi side Al Hilal, due to be hosted in Al Ain, was postponed for 24 hours because of the weather.
Bahrain, to the UAE's north-west, was also hit by heavy rain and flooding after being pummelled by thunder and lightning overnight.
"I like to play in the rain, but for the first time it scares me," said nine-year-old Ali Hassan, as he helped his mother clear water from outside their house in Bahrain's capital Manama.
The storms descended on the UAE, Bahrain and parts of Qatar after hitting Oman, where they caused deadly floods and left dozens stranded.
A child's body was recovered on Tuesday, bringing the death toll to 18 with two people missing, emergency authorities told the official Oman News Agency.
Nine schoolchildren and three adults died when their vehicles were swept away in flash floods, the news agency reported on Sunday.