The actress, who married Makhija in 2003, said her split was "amicable".
"To all those who care and especially those that don't my husband Munna and me have decided to part ways after 11 glorious years of marriage. Our split as some might call it is amicable and we hold each other in the highest esteem for now and forever," Pooja tweeted.
The 42-year-old actress, who is the daughter of Mahesh Bhatt, said she decided to go public with the split as she wanted her fans to know the story from her.