The spaceship was sent into a slumber in 2011 to conserve energy before it embarked on one of the most technologically advanced missions ever attempted - landing on a comet at 24,600mph.
A webcast showed jubilant scientists at mission control in Darmstadt,
"It was a fairy-tale ending to a tense chapter," ESA said in a press release.
If all goes to plan the probe will rendezvous with the comet in the coming months and drop its Philae lander docks onto its icy surface in November - a move that has never been attempted before.
The 2.5-mile-wide comet has almost no gravity, so the probe will have to use harpoons and ice anchors to clamp on to the surface.
The spacecraft was launched in 2004 on a trek of seven billion kilometres (4.3 billion miles) around the inner Solar System.
Comets are clusters of ice and dust which are believed to be remnants from the very birth of our star system.
Analysing the comet should unlock secrets of how the Solar System formed and possibly how life on Earth began.
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