According to the Met Department, inclement weather is expected to begin from the west by Wednesday night, extending over most areas of the country on Thursday
Bottas was .207 seconds quicker than world champion Hamilton, who leads Bottas in the standings by 47 points.
Encouragingly for Red Bull, Max Verstappen was only .246 behind Bottas in third with his Red Bull teammate Alexander Albon fourth in warm and sunny conditions.
Celebrating its 1,000th F1 race on a track it owns made little difference for struggling Ferrari, with Charles Leclerc 10th and Sebastian Vettel 12th. Vettel's engine cut out right at the end and he was left stranded on the side of the track.
The session was briefly suspended twice after minor crashes left debris on the track.
Approaching the halfway point of the 90-minute session, McLaren driver Lando Norris lost the rear of the car and went backward into the barriers.
Then about 15 minutes from the end, the red flag came out again when Kimi Raikkonen span his Alfa Romeo into gravel. Racing Point's Sergio Perez was just behind him and a crash was narrowly avoided. Both drivers were summoned by the stewards over the incident.
There is a third practice Saturday lunchtime ahead of qualifying in the afternoon.
Fans were present for the first time at the ninth race this season amid the coronavirus pandemic. The 3,000 spectators were split into three stands.
Mugello's 5.2-kilometer (3.2-mile) Autodromo Internazional usually holds Moto GP races and is hosting an F1 race for the first time.
The track is noted for its succession of fast corners. Leclerc and teammate Vettel did some testing there in June. Raikkonen, F1's oldest driver at 40, made his F1 testing debut for Sauber here 20 years ago.
Earlier Friday, Bottas was .048 quicker than Verstappen with Leclerc third and Hamilton fourth.
Pierre Gasly, who won his first race last weekend at the Italian GP in Monza, was fifth.
Vettel was a lowly 13th and Ferrari team principal Mattia Binotto tried to explain why.
"I think Charles (Leclerc) drove very well this morning, I think Seb's searching for confidence in the car a bit," Binotto said. "Which is the real Ferrari? I think it's neither one nor the other."
Haas driver Romain Grosjean almost crashed into the back of Perez's car and had to swerve suddenly to the left. Grosjean then sat out the last 30 minutes of P2 because of an electronic failure.
According to the Met Department, inclement weather is expected to begin from the west by Wednesday night, extending over most areas of the country on Thursday
The number of e& UAE subscribers reached 14.5 million in Q1 2024
National Emergency, Crisis and Disaster Management Authority confirmed its readiness to deal with inclement weather
He will be among a 15-member squad headed to the United States and West Indies for the tournament starting June 1
Most EVs promise mileage of 250-500km depending on engine variants and price points
Public health risk low but farm worker vigilance urged; drinking pasteurised milk advised to reduce risk of spread
PSG were dominant in a 2-0 win over Dortmund at home to open their Champions League campaign, but were held to a 1-1 draw in the return leg
Company aims to increase dividends by a minimum of 5% every year