The fire brigade said it received 300 '999' calls overnight as the "loudest ever" storm hit London and the south-east.
Twitter users say they had "never heard thunder like it" and the weather was so bad power had been lost in some areas.
Torrential rain also brought flooding and caused car alarms to "go off all over the place".
Many took to Twitter to say they had been woken up - and the hashtag #londonstorm quickly started trending.
The London Fire Brigade said it had experienced an "extremely high volume of calls to weather related incidents" in London between 1am and 3am.
But it urged people only to call 999 if it was an emergency.
A spokesman said: "Crews are being mobilised to incidents as quickly as possible but the Brigade is appealing to people to only call 999 in an emergency - where there is a risk to life or property."
The Environment Agency has issued four flood warnings covering rivers in Bromley, Sidcup and Basildon, and 22 flood alerts across of the South East.
Showers are expected to ease by 10am on Thursday morning before returning with similar intensity from 2pm.
The Met Office also issued an amber "be prepared" warning of rain for part of Kent, Sussex and Surrey effective until 6am on Thursday.
While a yellow warning covering the South East is in place until 6am on Friday.
With the bad weather they have already had, some spared a thought for Glastonbury revellers who may have been affected.
While others were grateful the storm had brought some welcome hayfever relief.