The former shadow equalities minister accused officers of racial profiling and said the force was "institutionally racist" after she and her friend were pulled over in Hackney, east London, on Sunday .
The MP for Brent Central, who recorded a video of the incident which was later shared widely on social media, claimed they had been pulled over by officers simply for "being black and driving a nice car".
But Scotland Yard's deputy commissioner Sir Steve House has defended the officers' conduct after reviewing the incident, saying they acted "professionally and politely".
He also said it was wrong that officers were facing "trial by social media".
Sir Steve said in a statement: "The officers in this case came into work on Sunday to keep Londoners safe.
"Officers expect to be scrutinised and there are existing, appropriate and proportionate processes for making complaints and for facts to be established, and on the occasions where there is fault - unlike this case - for consequences to follow.
"The increasingly routine trial by social media is unfair and damaging to individual officers and has the potential to undermine the role our communities need us to do to protect them and keep them safe from violence."
After the incident, Scotland Yard said the stop was a result of an officer having "incorrectly entered" the car's registration plate into a computer and wrongly identifying it as a vehicle registered to Yorkshire. The force said that, once the mistake was realised, the officer explained the situation and let the pair go.
Sir Steve said the officers "acted professionally and politely, explaining why the stop was made and, when realising there was a mistake, explaining this and continuing to answer the occupants' questions".
“Criminals often use vehicles to travel in and to commit crime, therefore officers will often check cars to see if there is anything that requires them to stop it and do further checks,” Sir Steve said.
“The officers ran a number plate check on the vehicle. At this stage, the officers still didn’t know who the occupants of the car were, including their ethnicity because the car windows were tinted.”
He also condemned abuse directed towards Ms Butler, including conspiracy theories suggesting the driver of the car was white, after the footage was shared.
He said: "It is unwarranted and unacceptable and we are working to support her.”
He also made clear that he had spoken with the Labour MP about her concerns over why the stop was made.
Sir Steve's comments echoed those of Metropolitan Police Federation chairman Ken Marsh, who urged force officials to release body-worn camera footage from the officers involved, saying: "We've got nothing to hide".
Can I just say a massive thank you for all who have offered support and solidarity on twitter,email,etc You have outweighed the abusive ones so thank you ❤ pic.twitter.com/nZTfMwFnRG— Dawn Butler MP✊🏾 (@DawnButlerBrent)August 11, 2020
The Met has come under pressure in recent months over a series of incidents that have led to racial profiling accusations.
The most high profile was a stop involving Team GB athlete Bianca Williams and her partner, who were asked to get out of their car while their small child sat on the back seat, which has been referred to police watchdog, the Independent Office for Police Conduct.
Sir Keir Starmer has said the Met Police must take allegations of racial profiling “extremely seriously”, and that the black community must have “trust and confidence” in the police following the incident on Sunday. Boris Johnson also said officers must treat people "fairly" but denied that the force was "institutionally racist".
Met Police commissioner, Dame Cressida Dick, has also rejected those allegations.
This week Ms Butler was named by Vogue magazine as one of the 25 most influential women shaping 2020 for her support of Black Lives Matter protests .
She described her backing of the anti-racism movement as having led to threats of attack on her office and staff having “drastically escalated”.
Agencies contributed to this report