This is the third cyclone-related death reported in the district.
The cyclone impacted Pune as it moved towards the northern part of the state on Wednesday, battering parts of Khed, Maval Mulshi, Junnar and Ambegaon tehsils.
Pune district had already recorded two cyclone-related deaths on Wednesday.
Narayan Ananta Navale, whose mother Manjabai was killed after a wall of their home in Khed tehsil collpased on Wednesday, died at a private hospital in Pune on Thursday, an official said.
"Three members of the family, including him, were injured in the incident at Wahagaon village," he said.
Earlier, Prakash Mokar (52), a resident of Mokarwadi in Haveli tehsil, had died while trying to catch hold of the tin roof of his home during the storm on Wednesday.
Meanwhile, two cattle were electrocuted in Mulshi tehsil and tin roofs of three schools and a gram panchayat office in Velhe tehsil were blown away by gusty winds.
Zilla Parishad CEO Ayush Prasad on Thursday said 57 anganwadis, 31 zilla parishad schools and four gram panchayats suffered damages during the cyclone. SPK ARU ARU