MEPs approved by 557 votes to 92 against with 29 abstentions a motion urging EU leaders to postpone a decision on whether enough has been achieved in talks in order to start discussing a future relationship, at their next summit starting on October 19.
With all the major groupings in the European Parliament backing the non-binding resolution, the result of Tuesday's vote was a foregone conclusion.
Barnier told the parliament in Strasbourg, eastern France, that May's speech had been "translated into negotiating positions" by her negotiating team led by Brexit minister David Davis.
But he warned of significant differences, in particular on how much Britain must pay as it leaves the bloc in March 2019.
And he rejected accusations by eurosceptic British MEPs that the EU was trying to hold Britain to ransom in the talks.