Ms Williams and Mr Dos Santos, both international athletes, were stopped by officers on July 4, 2020 as they drove to their west London home from training with their then-three-month-old boy in the back seat of their Mercedes.
The couple accused the force of “racially profiling” after being handcuffed and separated from their son during the stop, during which nothing was found.
The police watchdog ordered that five officers involved in the stop should face misconduct proceedings after footage of the incident sparked controversy, a move opposed by the Met.
PCs Pc Jonathan Clapham and Sam Franks were found by the panel to have breached standards over integrity and honesty after lying that they smelled cannabis while searching Mr Dos Santos.
Chairwoman Chiew Yin Jones said their conduct had breached standards of professional behaviour and thus amounted to gross misconduct.
Both were sacked by the Met within hours of the disciplinary panel's decision.
The panel found it not proven that Pc Clapham and Pc Franks breached the standards of professional behaviour in respect of equality and diversity.
The officers had told the panel they followed Mr Dos Santos in their police carrier because of the "appalling" and "suspicious" nature of his driving and were doing their duty when they conducted the stop and search.
Mr Dos Santos had told the hearing he had been targeted by officers because he was "DWB, driving while black" in a Mercedes.
Karon Monaghan KC, for the Independent Office for Police Conduct (IOPC), told the disciplinary panel at the start of the hearing that the watchdog's case would say there was "institutional discrimination" in the Met Police.
Mr Dos Santos told the panel while giving evidence that he had been "afraid" for the safety of his partner and his three-month-old son.
Body-worn footage of him swearing at the officers was shown during the hearing; he accepted his behaviour, saying: "Everybody deals with trauma differently."
The panel was told Mr Dos Santos was stopped nine times within four weeks of buying a car in 2018.
Mayor of London Sadiq Khan said the panel's findings would "anger and alarm many Londoners", and "just shows the scale of the challenge the new leadership team have to change the culture of the Met".
He called for lessons to be learned and said he would support the police force to deliver "urgent improvements".
The IOPC's Steve Noonan said he recognised the incident had "caused widespread community concern about the use of stop-and-search powers by police".
He added: "We know that black people are almost nine times more likely to be stopped and searched by police than white people, and nearly nine times more likely to be searched for drugs, despite a lower 'find rate' of drugs for black people than white people.
"It's figures like these and cases like Bianca and Ricardo's which emphasise why black people report having low trust and confidence in police."
Three other officers - Acting Police Sergeant Rachel Simpson, PC Allan Casey and PC Michael Bond - were cleared of gross misconduct by the panel.
Pcs Casey and Bond and Ps Simpson were found not to have breached any standards.
The misconduct panel found it proven that Ps Simpson asked Pc Franks if he wanted to take Mr Dos Santos into the vehicle carrier to "do a bit of a ferret around his groin and his shoes" to satisfy himself that everything had been searched, but it was found not proven that she breached the standards of professional behaviour in respect of authority, respect and courtesy.
Deputy Assistant Commissioner Matt Ward said: “The misconduct hearing panel, led by an independent legally qualified chair, has heard detailed evidence over five weeks to reach its conclusions today.
“While the panel accepted the officers’ version of events in most matters, including that their decisions were not motivated by ethnicity, it found that PC Clapham and PC Franks lied about smelling drugs on stopping the vehicle.
“Honesty and integrity are at the core of policing and, as the panel has concluded, there can be no place in the Met for officers who do not uphold these values.
“Mr Dos Santos and Ms Williams deserved better and I apologise to them for the distress they have suffered."
Earlier this year, Ms Williams won bronze in the 4x100m at the World Athletics Championships in Budapest, while Mr Dos Santos competed in the 400m at the Tokyo 2021 Olympics.