I was browsing a forum about Intramuros when I came across an old postcard of the Puerta del Parian (which I blogged last June 30th). The forum gave the names of the churches that can be seen behind the gate. It states:
Puerta del Parian: the old San Juan de Dios chapel had a nice dome to complement the nearby square cupola atop San Francisco Church.
Parian Gate Postcard
So the dome is that of San Juan de Dios chapel and cupola of the San Francisco Church, first built in 1602 and damaged in the 1645 earthquake; rebuilt from 1739 until 1750 and destroyed during World War II. This is the only church then with no Bell Tower. Enshrine here is the Nuestra Senyora de los Angeles (Our Lady of the Angels).
RELATED ENTRY:
Parian Gate Postcard