Pathanamthitta and Kottayam districts received the highest rainfall in the past year.
The IMD has predicted isolated cases of heavy rain with lightning.
The system is likely to hit the Puri coast (Odisha) as a deep depression after getting weakened inside the sea during its journey to the shore.
The cyclone, however, is weakining into a deep depression, reported IMD.
Very heavy rainfall is likely to start in north coastal Andhra Pradesh and south coastal Odisha by Friday evening.
The low-pressure area had developed over the Andaman Sea on Nov 30. It intensified into a depression on December 2 and further into a deep depression on Friday morning. It turned in a cyclone on Friday noon.
The Met Department has warned fishermen not to venture out to the sea along Kerala's coast on Tuesday.
The two districts wherein the alert was not sounded are Kollam and Thiruvananthapuram.
On Monday, the yellow alert is in force in the districts of Kottayam, Idukki, Ernakulam, Thrissur, Palakkad, Malappuram, Kozhikode, Wayanad, Kannur and Kasaragod.
Only moderate rainfall expected in the state between December 3 and 9.