The roundabout, which saw more than 80 collisions and 90 people injured in 2012-14, was replaced with two-way traffic on Sunday.
Transport for London (TfL) said congestion was due to "traffic getting used to the new layout".
"It's a very busy junction and it always will be," a spokesman said.
The reintroduction of two-way traffic at the junction for the first time in 50 years was a "key milestone" in the £25m transformation at Elephant and Castle, TfL said.
In addition to the new road layout, left turns from Newington Causeway towards New Kent Road and right turns from New Kent Road to Newington Causeway have also been banned.
But road users took to Twitter to complain about their Monday morning commute.
"It's 8am and the queue for the new #elephantandcastle junction starts somewhere south of Camberwell. allow extra 1hr 4 journey (or walk!)", a Twitter user posted.
"Shock horror! All approaches to Elephant and Castle worse than ever. Only TfL could spend millions and millions to make something worse!" tweeted @tango97.
Andy Woodward tweeted: "Delays around Elephant and Castle even worse today. If this was the tube there would be outcry. Commuters use buses too!"
Road users had been advised of traffic changes with a countdown to the traffic switch and advisors and police were on site to help keep traffic moving, the TfL spokesman said.
A spokesman for London TravelWatch said: "It's early days - we need to wait and see how it pans out."
TfL plans to convert the space created by removing the roundabout into a new public area.
It will replace subways with new pedestrian crossings, create new cycle routes and introduce a 20mph speed limit, TfL said.

The 39-year-old Englishman has not played in a competitive match since the World Championship quarter-finals in April, and has not entered next week's UK Snooker Championship.
"I do want a place within the sport, and I'm trying to fathom what that place is," he told Eurosport.
"I'm trying different things."
O'Sullivan also opted not to defend his title at last week's Champion of Champions in Coventry, which Neil Robertson won.
He is currently playing exhibition matches.
"It's been tough at times but I truly feel I have a good idea of what it is I want," he said. "I don't want the pressure of being the top man in snooker any more. I feel that should be left to the new generation of players.
"It's funny really. I'm actually enjoying my practice more then ever. I play for fun now. I still try to be the best I can be, but I don't have to be so serious about being so committed to it.
"Me and my mates play a lot these days."

The A40 between Nantgaredig and Whitemill is closed and diversions are in place following the incident at about 18:15 GMT on Friday.
A grey Smart Fortwo Prime, a black Volkswagon Golf and a grey Volvo were involved in the crash.
Dyfed Powys Police are appealing for witnesses.
The removal of the Elephant and Castle roundabout has been causing chaos for commuters, with motorists complaining of queues of more than an hour.
[NEXT_CONCEPT]
Five-time world champion Ronnie O'Sullivan says he no longer has any interest in being snooker's "top man" but has not retired.
[NEXT_CONCEPT]
Four people have been taken to hospital after a three car collision in Carmarthenshire.