The Oscar-winning actor and the Czech model - who had a brief fling in February 2008 - are said to be giving their relationship another go and have been seen on several dates together.
Petra, 32, split from fiance Jamie Belman last month and was soon comforted by 51-year-old Sean Penn.
The pair - who briefly dated during one of the actor's splits from now ex-wife Robin Wright - were recently seen enjoying a dinner in New York.
A source said: ''Petra was all over him like crazy. She was rubbing his shoulders and rubbing his leg. She was hanging all over him. Sean looked like he was playing it cool. But they did leave the restaurant together.''
Petra survived the 2004 tsunami in Thailand, which tragically claimed the life of her then-boyfriend, photographer Simon Atlee and has since been romantically linked to singer James Blunt and director Peter Berg.
Sean was most recently linked to Scarlett Johansson.