© BBC NewsWitnesses said cars in Balcarres Street were bobbing about in the water.
The downpour turned streets in Morningside, Colinton and Oxgangs into rivers and caused an estimated £100,000 worth of damage to vehicles at a car showroom.
Emergency council workers joined firefighters to deal with the flooded areas while a number of bus services had to be diverted.
One of the worst hit areas was Balcarres Street in Morningside, where the flooding began just after 2.40pm. Shaun Robertson, 22, and Lee Craig, 26, both painters and decorators, were trapped in their van in the middle of the road for over an hour.
Mr Robertson said: "We were driving through as we'd just done a job on Balcarres Street when the water started rising pretty quickly and we were stranded in our van.
"The electrics went off and we were left stuck. In the space of around ten minutes the water had gone from a few inches to being up around the doors, I've never seen anything like it in my life."
One resident in Balcarres Street said her ground-floor flat had been ruined following the flash flood, while another told how her fish had been washed away from her garden pond. Communal wheelie bins were also seen floating away as pedestrians battled through waist-high water.
Another resident said: "The house is filled with water, so we've had to spend the afternoon scooping it out. This has happened a couple of times in the street, which is why some of the tenements have flood blockers around their doors. The drains have completely clogged up and I've been told there's an underground river system below us."
John Mason, the service manager of the Saab showroom on the street, said vehicles worth £100,000 on the forecourt had been written off.
He said: "The cars out on the front are gone, but luckily most in the showroom are saved. It's happened before, around ten or 12 years ago, and apparently it was worse than this. I'm relieved I didn't park my car on the street this morning. The drainage outside is clearly not good and, because the cemetery opposite is on a hill, the water that's gathered has run down into our street.
"We were due to move premises next week to Colinton Road so we probably won't reopen, there's too much damage.
"It was extraordinary how fast the street filled up, in a matter of three minutes it was covered in water. It's the most severe flash flood I've seen."
Aileen Murray, business manager of PF Counselling on Balcarres Street, added: "The rain was really lashing down and the water level rose dramatically - all within half an hour. We saw a guy have to climb out of his car."
Residents in Colinton Mains Drive described waste water pouring out of overflowing drains into their homes while locals stripped off their shoes and socks to wade through the streets.
Amanda Roy, 48, who lives in a ground-floor flat with her staff nurse husband, Robert, also, 48, said: "The road looked like a river. People from the council were down and they were talking about sandbagging the street at one point."
Meanwhile, staff at the Scottish Parliament said an apparent lightning strike at the building had caused electrical faults.
George McKendrick, operations manager for Lothian Buses, said the firm had deployed all its spare vehicles to cover services that had been disrupted. Services at Greenbank were diverted because the Braid Burn had burst its banks, while problems were also reported on Slateford Road and at Napier University's Craighouse Campus. The Met Office said that 17ml of rain had fallen in three hours compared with the July average of 74ml.
More rain was expected today, though not of the same intensity. There is a chance of showers tomorrow but they are less likely to be as heavy as the two preceding days.
The Scottish Environment Protection Agency (Sepa) issued flood warnings for Edinburgh and Lothians but said the risk from rivers was very low.
A Sepa spokeswoman added: "The risk of flooding from rivers is low at the moment because the river levels are already low. The main risk is from surface water on roads, and drains and culverts becoming overloaded."
A council spokeswoman said they had received a "significant" volume of calls from residents and business and had deployed emergency staff to help.
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