FA chairman Greg Dyke has laid a wreath at Hull-born Morley's grave at the now disused Barnes Cemetery in London.
Morley was the catalyst behind the meeting at London's Freemasons' Tavern in 1863 that led to the foundation of the FA.
He drafted the first laws of the FA at his home in Barnes and was elected as its honorary secretary from 1863-1866. He became the second president of the organisation from 1867-1874.
Dyke said: "Today is a fitting final act of the FA's 150th anniversary and a magnificent example of how far the game has come.
"Throughout the year we have celebrated the Football Association's rich heritage and looked to the future through the wonderful array of grassroots initiatives the FA and its county FAs help to run week in, week out.
"All year we have been celebrating 150 years of The FA, and of football, but none of this would have been possible without Morley. We all owe him a great debt. What he did to set football on its incredible journey to become the only true global game was a truly remarkable achievement."
The ceremony was followed by a boys, girls and disability football festival with a commemorative match between local children from Richmond Park Academy and Christ's School.
The FA has also released details of its National Game Strategy, the £200million investment into grassroots football.
Figures released by funding body Sport England last week that the number of adults taking part in football had declined by almost 200,000 since 2005.
The FA said its strategy, launched in 2008, has led to the creation of 4,132 additional mini-soccer teams, 1,010 new disability teams and over 650 FA standard charter clubs.