On his first visit to Mumbai after taking over as BJP president, Shah drove to Matoshree, the Thackeray family residence in suburban Bandra and met Uddhav.
Shah arrived at 10 pm, almost half an hour behind schedule.
Maharashtra BJP president Devendra Fadnavis and leader of the opposition in Maharashtra legislative council Vinod Tawde accompanied Shah.
The very fact that they met signals that the more than two decades-old alliance is still on track, a senior Sena leader said.
Until Wednesday, it wasn't clear if Shah would meet the Shiv Sena chief at his residence, which has almost been a tradition with top BJP leaders visiting Mumbai, since the Matoshree visit did not figure in Shah's elaborate minute-by-minute schedule.
However, Tawde had announced on Thursday morning that Shah had accepted Uddhav's invitation and would visit Matoshree.
Shah also visited the memorial (Smriti Sthal) of late Bal Thackeray at Shivaji Park.
Buoyed by the results of Lok Sabha polls when BJP earned more seats than Shiv Sena in Maharashtra, BJP has been looking for a better share in the seat-sharing formula for assembly elections due in the state in October.
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