This comes after opposition called the vote fraudulent and demanded a re-run. They also threatened to protest, something the observers urged against.
The final result is expected in the next few days.
It was the country's second democratic presidential election since it gained independence from France in 1958.
The EU's chief observer, Frank Engel, said he hoped Guineans remember this as a "milestone" in their "young democratic institutions".
But he also said there were many shortcomings, including problems with voter registration.
Mr Engel added that the lack of transparency had led him to lose confidence in the electoral commission, and that he would be watching to see the results were announced in a suitable way.
The EU observers have asked that any grievances are directed at the courts, not aired on the streets.
Several people were killed in clashes during the election campaign.
Alpha Conde was standing for a second term after becoming president in 2010 in the country's first democratic election.
Mr Conde had spent the previous decades fighting authoritarian regimes, during which time he was both exiled and imprisoned.