Mr Poroshenko (C) said the pact was a “symbol of faith and unbreakable will”
Ukraine, Georgia and Moldova have signed partnership agreements with the European Union, in a move strongly opposed by Russia.
The pact – which would bind the three countries more closely to the West both economically and politically – is at the heart of the crisis in Ukraine.
Russian President Vladimir Putin said making Ukraine choose between Russia and the EU would split it in two.
A ceasefire with pro-Russian rebels in east Ukraine is due to end on Friday.
Mr Putin called for a long-term ceasefire to allow talks between the government and separatists.
Meanwhile the United Nations refugee agency said there had been a sharp rise in the numbers of displaced people in eastern Ukraine in the past week, with 16,400 people fleeing the area.
The total number internally displaced has reached 54,400, while a further 110,000 people left Ukraine for Russia this year.
Analysis: Steve Rosenberg, BBC News Moscow
There is a general sense of irritation or perhaps even anger here that Moscow has failed to convince countries like Ukraine, Moldova and Georgia not to sign this historic free trade deal today with the EU.
Moscow has economic concerns about these deals – it is worried that the Russian market could be flooded by cheap goods from the EU that would hit Russian producers.
More pressing for Moscow are the geopolitical concerns here – the whole idea of former Soviet states, countries that Moscow still views as being within its sphere of influence, drifting towards Europe and one day possibly becoming part of the EU – that really grates with Moscow, particularly in the case of Ukraine.
There’s a lot of concern about what could happen in eastern Ukraine – the ceasefire announced a few days ago by Mr Poroshenko, and the ceasefire announced by armed separatist rebels, is due to expire today. It’s unclear how things are going to develop later.