Many complained they were separated from their luggage, prevented from leaving the airport and were not given food or water during delays of up to 15 hours.
This morning dozens of passengers were pictured sleeping on the aiport floors as more cancelations and delays hit the West Sussex airport. Passengers should check their journeys before travelling.
"We would advise passengers not to travel on the Midland Main Line over the weekend unless absolutely necessary".
The official top temperature that day - and a new July record - was 38.1C, in Cambridge.
European air traffic co-ordinating agency Eurocontrol said the problem was caused by an "issue with radar displays".
"Flights are now arriving and departing at Heathrow, and we are supporting NATS to resolve the issue as quickly as possible".
Gatwick Airport advised passengers to check with their airline for updates.
Gatwick also posted on Twitter this morning, writing: "Good morning from Gatwick!"
Rail delays caused by extreme heat also began to ease on Friday.
Network Rail engineers worked overnight to fix damage at several locations after the temperature of steel tracks soared to up to 20C higher than the air temperature, while overhead power lines also suffered heat-related damage.
"For the latest status of your flight please check with your airline".
Train company Govia Thameslink Railway has sparked a row after refusing to pay compensation to season ticket holders who took its advice not to travel during yesterday's scorching temperatures.
Yesterday's record temperatures caused major disruption to train services.
"The hot weather forecast this week means Network Rail has activated its 'extreme weather action teams" (EWATs) to ensure passenger safety and that we keep our railway running as reliably as possible'.
"We apologise for any inconvenience people may be experiencing, and will provide further information as soon as possible".
Rail track temperatures in direct sunlight can often be up to 20 degrees higher than the air temperature.
"The thunderstorms could continue on and off through the course of the day", Met Office meteorologist Greg Dewhurst told PA.
The warning area has been extended to cover the Central Belt as well as western and southern Scotland, along with much of England away from the south west.
Rail passengers in the Midlands are facing severe delays as customers are warned not to travel.
The majority of trains between London Euston and Milton Keynes Central are now showing as delayed or cancelled.
Passengers using Eurostar services to and from Paris also faced "severe disruption" due to overhead power line problems in the French capital.
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