Rossi and factory Yamaha team-mate Jorge Lorenzo lost out to the works Hondas of Dani Pedrosa and Marc Marquez, with the latter beating Lorenzo to second place in controversial circumstances.
"Here in Jerez I expected we could go faster than Honda but they were in front of us," said Rossi, who finished fourth.
"It was a difficult race. Unfortunately we were not able to be better, we suffered a bit with the conditions."
Rossi added that Yamaha will have to work hard to make up its performance deficit to Honda, starting with Monday's post-race test.
"We still have some work to do to improve the bike," he said. "Tomorrow we have the test and we'll try to find the right balance."
Lorenzo believes he got the most that he could out of the Yamaha package.
"I did my best, every lap every corner I pushed 100 per cent," said the reigning champion.
"We still don't have a very competitive bike. We need to improve it."
Yamaha team director Massimo Meregalli said that the team will focus on tyre life during testing on Monday.
"We really worked as hard as we could to improve tyre life," he said. "Unfortunately we couldn't get what we were looking for.
"We will focus some more effort during the test to fix it for the rest of the season.
"The season is long. We lost a battle but not the war."
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