The Modern Family actress announced the split with a screenshot of a note on her Who Say account on Friday.
"Not that anyone should care, but in order to not give the press the chance to invent crazy and hurtful drama, I prefer to tell my fans personally that Nick and I have [decided] to be apart," she writes.
"We have [been] having too many problems with figuring out how to spend time together and [because] of my work and now his, its been getting worse and worse, not fun anymore."
The Colombian bombshell, 41, says that despite their separation, the two remain good friends. "We are still very close but we [believe this] is the best thing for us right now," she adds.
A source tells PEOPLE that the two had been weathering a rough patch for some time now.
"Nick and Sofia were always on rocky grounds, especially in the last year or so," the source says. "It has been worse since she has become a real superstar and is so busy and in demand everywhere. It's hard for them to have a normal relationship, much less spend enough time together."
In February, the actress was still deciding on plans for her dream wedding with Loeb, saying she was unsure about the exact details. "It's either I do something really big, or I do something really small with Nick and I and my son, and then my mom, and then my cousins, and then it's impossible," she told Ellen DeGeneres.
Already mom to son Manolo, Vergara had been open about having a baby with Loeb, turning to a fertility doctor for help in expanding her family.
"Hormone pills, and then after that it is hormone injections. They want to get as many eggs as they can because usually you produce them but they’re not good," she told Vogue magazine of freezing her eggs. "They have to be perfect, perfect, perfect ones."
With reporting by LINDA MARX