The nine-time world champion, given the all-clear to take part after passing a mandatory medical examination at the MotorLand Aragon circuit, took it easy in the opening session staged in damp conditions.
Rossi, who had completed 20 training laps in Misano on Tuesday, came in 20th, more than two seconds back.
But in Sunday's practice he almost hit the tarmac, somehow maintaining his balance as Rabat touched his back wheel at turn 14 - the Spaniard unable to do the same as he went sprawling across the track.
"It was really hard", said Marquez, who began fifth on the grid.
"Since the first lap I felt not so good, I was fighting against the bike all the race". I was fighting against the bike and almost crashed many times.
One of Marquez's near misses saw him try to pass Valentino Rossi for second, only to get out of shape and forced to steer inside race leader Jorge Lorenzo, sending him wide on the exit and to the back of the four-man lead group.
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"Even on the last lap I saw that he was only 0.8s [behind], I mean still he believed but I was trying to manage the risk with the distance".
"Rossi made a unusual movement towards me, closing my space at a speed of 300 kilometers per hour.it's not good, but I managed to overcome it and able to compete for the podium, "said Pedrosa quoted from Sky Sports". Marquez and Dovizioso were tied for the lead entering the weekend. Fifth-place Rossi is 56 points from the lead.
Nevertheless, Pedrosa remain pleased with the results obtained in the 14th series of 2017 MotoGP racing.
Then he went after Lorenzo and blitzed the Ducati rider for his fifth win of the year.
"The main opponents for the championship lost some points, so we opened a small advantage and it's very important to arrive in Japan with that very small advantage", Marquez said.