Liverpool boss Rafael Benitez said: "It was a good result but then we had the bad news about Martin.
"He's had X-rays and they confirmed he has a broken metatarsal. We have to check over the next couple of days how long it will take to recover."
Your reaction to Skrtel's injury Skrtel was injured in second-half clash with Antonio Semedo as the Reds won 3-1 in Romania to reach the last 16 with a 4-1 aggregate score.
He has been a mainstay of Liverpool's central defence this season, featuring 29 times and scoring one goal in the 2-2 draw at home to Manchester City in November.
There was better news from Benitez about Skrtel's fellow defender Glen Johnson.
The £17m signing is nearing a comeback, having not played since late December because of a knee injury.
"He's doing well. He was training today with the team - a light training session," said Benitez.
"I was watching him and he was quite sharp but Sunday will be too soon."