Ponting's score came from 103 balls and included six fours, leaving Australia 34 runs behind with eight second-innings wickets remaining at Headingley.
Resuming on 62-2 after tea, Ponting and Michael Clarke, on 32 not out, counterattacked until bad light halted play.
Earlier, Shane Watson took career best figures of 6-33 as Australia dismissed Pakistan for 258 in its first innings, in reply to Australia's initial total of 88.