Mosques in Woolwich, Braintree in Essex and Gillingham in Kent were also attacked with bricks while anti-Muslim extremists threw bottles at cops in ugly scenes.
More than 100 EDL members chanted “E-E-EDL” as two men were arrested in south-east London.
While a 43-year-old man is in custody on suspicion of attempted arson after reportedly walking into a mosque with a knife in Braintree, Essex.
Another man in Kent is in custody on suspicion of racially-aggravated criminal damage.
EDL leader Tommy Robinson, who headed a group of around 250 men, ranted: “They’re chopping our soldiers’ heads off. This is Islam. That’s what we’ve seen today.
“They’ve cut off one of our Army’s heads off on the streets of London.
“Our next generation are being taught through schools that Islam is a religion of peace.
“It’s not. It never has been. What you saw today is Islam.
“Everyone’s had enough. There has to be a reaction, for the Government to listen, for the police to listen, to understand how angry this British public are.”
The secretary of the Braintree mosque, Sikander Saleemy, said he felt like it was a “revenge attack”.
He said: “The police said it’s too early to try and link it to what happened in Woolwich, but those of us who were here feel that it was some sort of revenge attack.
“It was clear from the man’s behaviour. We absolutely condemn what happened in Woolwich, but it had nothing to do with us.
“It was an appalling act of terror - but it wasn’t 'Islamic' in any way. I wish it wasn’t described like that, because sadly people will now start to blame Muslims.”