About 3,000 officers were deployed as the group walked from Queen Elizabeth Street, over Tower Bridge, to Aldgate.
Police said 14 people, mainly from the EDL, were arrested for public order offences during the march.
By 19:40 BST, police said about 150 counter-protesters had been arrested for diverting from their agreed route.
On Friday, the EDL lost a court battle after police cut short the route of its planned march through the Tower Hamlets area, which has one of the biggest Muslim populations in the country.
Hundreds of anti-fascist demonstrators gathered at a park in Aldgate East to protest against the shortened EDL march.
"There have been 14 arrests as part of the policing operation for the demonstrations," a police statement said.
It added: "In addition we have made approximately 150 arrests for breaching  section 12 and section 14 of the Public Order Act 1986. All these approximately 150 people were protesting against the EDL presence."
A tweet on the EDL website stated: "Tommy's been arrested for incitement."
The anti-EDL gathering took place at the Altab Ali Park in Aldgate East, and was also attended by the mayor of Tower Hamlets, Lutfur Rahman, and John Biggs, a Labour London Assembly member.
Mr Rahman said he was "very fed up" with the EDL's demonstrations in the area, adding: "We are a united community and we are a diverse community. Young people are not coming out today because they are frightened."
BBC London home affairs correspondent Guy Smith said Met officers formed a "security envelope" around the EDL with a strategy to "keep both sides apart".
It took the police to the High Court after the Met shortened the route of Saturday's march over concerns of "serious public disorder".
Mr Robinson said he would hold sponsored walks in east London to raise money to pay for the court costs.
English Defence League (EDL) leader Tommy Robinson has been arrested as about 500 supporters of the far-right group held a march in east London.