The 23-year-old was a free agent after leaving the Shrimpers in December.
The Czech started his professional career with Liverpool before joining Yeovil in June 2014, making 45 league appearances for the Glovers.
He will be unable to play for the Pilgrims, who have not disclosed the length of his deal, against the Reds in the FA Cup third round, having already played for Southend in the competition.
Find all the latest football transfers on our dedicated page.
Plymouth Argyle have signed former Southend United defender Jakub Sokolik.