The British-built unmanned probe, which was launched June 2 from the former Soviet space port in Kazakhstan, is scheduled to land on Mars' surface on Christmas morning.
"I'm very proud to say we have made a big step toward getting to Mars, but this is really only the beginning," said David Southwood, the European Space Agency's director of science.
In the control room, screens flashed to red to confirm the lander was on its way after separating from the Mars Express spacecraft.
"It was a relief, absolutely, we have all been waiting for this moment for a long time and when our screens lit up, we were ecstatic," Mars Express mission official Zeina Mounzer said.
The mission is the first to try to determine if there is life on Mars since the United States sent the Viking I landing craft to Mars' surface in 1976.
"It's not looking for little green men, but it is looking for matter that might provide evidence of life. It is looking for clues," Southwood had said earlier.
Friday's maneuver was the first in a series of critical navigational moves on which the success of the mission depends. The spacecraft gently pushes the probe away, setting it spinning to maintain stability as it heads toward Mars.
The lander is expected to reach the surface early on Dec. 25.
About the same time, engineers plan to fire the main engine on the Mars Express craft for about 30 minutes, putting it into a 250-mile-high orbit. As it circles Mars, the spacecraft will use radar to penetrate the surface looking for layers of water or ice.
"This if the first time we will be looking under the surface of Mars using radar from Mars Express," Southwood said.
Of 34 unmanned American, Soviet and Russian missions to Mars since 1960, two-thirds ended in failure. In 1976, twin U.S. Viking landers searched for life but sent back inconclusive results.
Earlier this month, Japan was forced to abandon its troubled mission to Mars, which was to determine whether the planet has a magnetic field, when officials failed in their attempts to position their Nozomi probe on course to orbit the planet.
The Mars Explorer, which cost about $345 million, is an attempt to demonstrate that Europe can have an effective and relatively inexpensive space program.
Since its June launch atop a Russian Soyuz-Fregat rocket from the Baikonur cosmodrome in Kazakhstan, the Mars Express has weathered solar eruptions that bombarded it with high-energy particles, temporarily disrupting its computers, as well as an unexpected drop in electrical power.
The 143-pound Beagle 2 named for the ship that carried naturalist Charles Darwin on his voyage of discovery in the 1830s will use a robotic arm to gather and sample rocks for evidence of organic matter and water, while Mars Express orbits overhead.
During its working life planned for one Martian year, or 687 Earth days engineers hope Mars Express will send back detailed overhead pictures of the planet's surface.
Scientists think Mars, which still has frozen water in its ice caps, might have once had liquid water and appropriate conditions for life but lost it billions of years ago. It is thought water may also still exist as underground ice.
U.S. officials are discussing a new course of space exploration, and debate has focused on whether the United States should set its sights on returning to the moon or landing on Mars.
By Melissa Eddy