Along with Maddox, their adopted four-year-old son, the couple left the Le Meridien hotel's basement and got into the auto-rickshaw at around 5.30 p.m., a local photographer told.
He said it was a meticulously planed quick exit from the hotel where they are put up in six suites on the fifth floor with round-the-clock security.
He also said the celebrity couple drove towards Saurabh Hall while two personal bodyguards in another auto-rickshaw tailed them.
"Nobody on the road took any notice of the famous couple," the lensman said.
The photographer who chased the star couple on his motorbike from a distance caught up with their three-wheeler even as he feared their bodyguards, who had roughed up a foreign photographer Saturday.
However, heavy traffic helped him to click photographs of the reclusive stars, he added.
Angelina, Brad and Maddox took the ride to the posh Poona Club area, then turned to the Inox cinema multiplex towards the University of Pune area.
"It was a fun ride for the close family as the sky had cleared and the evening sun creating a pleasant, cool atmosphere for the couple," said a member of the hotel's staff, who asked not be named.
They were back at the hotel within an hour, he added.
This is the second time the couple sneaked out of the hotel since they arrived here Thursday to shoot a film on American journalist Daniel Pearl who was slain in Pakistan in 2002.
Angelina is set to play Marianne, Pearl's widow, in the film "A Might Heart".
Producer Andrew Eaton and Hollywood actor Dan Futterman, who will play Pearl, had a series of production meetings with the couple on the fifth floor amidst tight security Sunday.
The big budget film's director Michael Winterbottom and other technical crew are arriving for the film's shooting, which is likely to begin Monday.