The couple underwent IVF in 2013 and Vergara's fertilised eggs have since been kept frozen in a fertility clinic in Beverly Hills.
The couple separated in May 2014 and a year later Loeb sued Vergara for custody of the embryos, using pseudonyms that were later leaked.
The twist in the legal battle came on Tuesday (US time) when the new right-to-life lawsuit, which also lists James Carbonnet as the embryos' "trustee", was filed.
Vergara, who earns US$43 million a season for Modern Family and is now married to True Blood actor Joe Manganiello, has strongly argued against Loeb's wishes.
"A child needs a mother and a loving relationship with parents who don't hate each other," the Colombian-born actress has said previously.
"I wouldn't want to bring kids to the world where it's already set against them. It would be so selfish."
The saga has provoked debate in America about when life starts, who should have the power to end it, and whether men should have the same rights as women over frozen embryos.
Loeb argued in a New York Times opinion piece, published in April 2015, that he should have equal rights over the two embryos, and accused his former girlfriend of wanting to keep them "sitting in a freezer until the end of time". He claimed that this would be "tantamount to killing them".
Vergara hit back and last month a judge in California upheld her request that Loeb name two of his former girlfriends who had abortions more than 20 years ago. Vergara's lawyers want to prove that Loeb has not always held a pro-life stance.
Loeb appealed against the decision, but the Court of Appeal backed Vergara, whose legal team wants to question both women under deposition to investigate his sexual past.
He has argued that it is unfair to name the women due to the high-profile nature of the case, and warned they could face intense scrutiny and shame.
The Daily Telegraph has contacted Vergara's representatives, who are yet to comment.