The 22-year-old has agreed a four-year contract and will join up with his new team mates for pre-season training on June 29.
“Juanmi is a young, exciting and attacking player who fits into the club’s strategic plan perfectly," Southampton executive director of football Les Reed told the club's website.
“He has been tracked closely by our recruitment department for some time, and we were keen to act quickly when presented with the opportunity to bring this young player with international quality to Southampton."
Juanmi, who scored eight goals for Malaga in 34 La Liga games last season, made his Spain debut this year in a friendly against the Netherlands.
"It’s a pleasure to be here and I am looking forward to being a part of this club," he said.
“I am anxious and I want to start as soon as possible. This is a big club and it has shown a lot of trust in me."
Southampton finished seventh in the Premier League last season under Dutch manager Ronald Koeman.
(Reporting by Ed Osmond, editing by Toby Davis)
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