Marquez was fastest in both Friday sessions at Losail, while his factory Honda team-mate Dani Pedrosa struggled for pace, failing to get into the top five in either session.
Rossi said Marquez had benefited from slipstreaming his Yamaha in practice two, but that his pace was real.
"In the second practice it was a gift from me because he came in behind," said Rossi.
"But like I said before, he's very strong. It looked like the Hondas had some problems yesterday and today but he is at the front anyway.
"That means he is very, very fast."
Seven-time MotoGP champion Rossi was third in two of the three sessions so far and fourth in the other. He believes a front row qualifying spot will be essential.
"The main target for me is to try to start from the first row, but I don't know if that will be possible because Jorge [Lorenzo] is very fast, he is very strong over a lap, and I expect the Hondas to be very strong," Rossi said.
"If I cannot start on the first row, it will be important to be close to it because I have a good rhythm so I can do a good race, but I have to start in the first five."