Nadal is seeking a third consecutive claycourt title of the season after winning the Barcelona Open and Monte Carlo Masters but his preparation for the tournament in the Spanish capital has been interrupted by the infection.
"On Friday I woke up at three in the morning with pain, a discomfort I had never felt before," the 14-times grand slam winner told a news conference on Monday.
"I went to the doctor and he told me I had an ear infection. It's nothing important but it is bothering me, it has caused me headaches and I've been feeling dizzy.
"Today I felt better and was able to train well for two hours. My aim and the tournament's was to start on Tuesday but after this it's better to wait a day and start on Wednesday."
If he gets past Fognini, Nadal could face Australian Nick Kyrgios in the third round, with Milos Raonic or David Goffin among his potential quarter-final opponents.
"The draw isn't ideal but the fact I'm playing at home is a plus," added the Spaniard, who has won the Madrid Open a record four times.
"I'm very happy with my start to the year, and not just the claycourt season. These have been very good months since I started playing on clay because I've been able to win tournaments after losing finals."
(Reporting by Richard Martin, editing by Ed Osmond)
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