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.
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Australian half-back Miller, 23, arrived from Hull FC in 2014 and his previous deal was due to expire at the end of the current season.
Tonga prop Fifita, 27, joined from NRL side Cronulla Sharks in June 2016 and his new contract includes an option for an additional year.
"Fifita has become an important member of the squad," said boss Chris Chester.
"He has so much passion for the club both on and off the field which is great to see.
"Jacob is still a young player with exceptional talent - I am looking forward to working with him for another two years and see him improve even more."
Plymouth Argyle have signed former Southend United defender Jakub Sokolik.
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Wakefield Trinity duo Jacob Miller and David Fifita have both signed new two-year contracts.