"They were in a bit of a rough patch for a while," a pal close to the Factory Girl actress revealed to Us Weekly.
Adding: "Their schedules on top of raising a child started to get to them."
Sienna, 33 and Tom, 29, started dating quietly in 2011 and welcomed their daughter Marlowe, the following year in July.
The actress was particularly candid in an interview with Time Out London about the challenges of motherhood.
"It's a shock, of course it is. Some people find it really easy, but for me I found it really hard," the British bombshell told the publication.
But the mother-of-one wouldn’t change a thing, speaking affectionately about her little one to Vogue at the beginning of the year, she beamed: "It was like, 'There you are - that's what I have been missing.''
"Like we're both in on something only we know. An amazing sense of being complicit with a little being."
The American Sniper star hinted there may be trouble in paradise when discussing her role as Taya, the widow of Bradley Cooper’s titular character, Chris Kyle, in the hugely successful Clint Eastwood film.
"I had a huge amount of empathy for Taya. To be going through motherhood on her own, not knowing whether her husband would survive every day, I can't imagine how difficult that would be."
Sienna and Tom are believed to have had an amicable break-up.
Before meeting fellow actor Tom, Sienna’s love life often attracted attention, particularity her tumultuous on-off relationship with British actor Jude Law from 2006 to 2011.
The 33-year-old starlet has yet to make a comment on the news, however she seems to be taking the break-up in her stride and was recently spotted at Wimbledon rubbing shoulders with Ari Emanuel - the Hollywood super-agent that inspired Jeremy Piven’s character in Entourage.