The 24-year-old left-back played only nine games for Villa after signing from Shamrock Rovers in 2012.
"Enda brings a lot of quality and adds balance to the left-hand side," manager Paul Cook told the club website.
The Republic of Ireland under-21 international rejected other offers from League One clubs before opting to join Pompey.
"This was a no-brainer because of the size of the club and the manager's aspirations for it," he said.
"It's easy to forget that this is a League Two club when you walk around the place and hopefully we can start to move back up the divisions."
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