The aircraft, set to leave for Edinburgh at 4.20pm, was surrounded by fire engines as people rushed from their seats.
Dramatic pictures show the condensation spreading into the plane.
An easyJet statement said: “Flight EZY017 from Luton to Edinburgh remained on stand after boarding due to a technical issue which resulted in mist caused by condensation being emitted into the flight deck.
“Passengers disembarked normally and as a precaution only are being transferred to an alternative aircraft which will be departing shortly.
“The safety of its passengers and crew is easyJet’s highest priority and easyJet operates its fleet of aircraft in strict compliance with all manufacturers’ guidelines.
“We would like to apologise to passengers for the delay and inconvenience caused.”
It came after a torrential downpour sent water gashing into the terminal building.
Rain could be seen leaking from the ceiling as passengers traipsed through large puddles.
The UK faced its first major storm in four months, with 60mph winds set to cause hazardous conditions for drivers this weekend.
Love Island’s Zara McDermott and her Made In Chelsea boyfriend Sam Thompson were caught up in the chaos at Luton Airport.
“Mist caused by condensation was emitted into the flight deck”
The reality TV stars posted on social media footage of the water pouring through a restaurant’s roof in the terminal this evening.
Zara said with the clip: “The roof is coming down in Luton Airport wtf. Sat in Bella Italia.
“I cannot believe this is happening, was just trying to enjoy my pizza.”
An airport spokesman said: “Following a period of unprecedented rainfall, we have experienced water damage in a number of locations.
“We apologise for any disruption to services while we seek to resolve the issue.”