The 22-year-old arrives at St Mary's from Primera Division club Malaga, for whom he scored eight league goals last season.
A series of tweets published through Saints' official account confirmed the upcoming transfer of the player who won the Under-19 European Championship with Spain in both 2011 and 2012.
The diminutive striker, who graduated from the Malaga academy, told saintsfc.co.uk: "It's a pleasure to be here and I am looking forward to being a part of this club.
"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.
"The training ground is magnificent and likewise the stadium
It really, really is a big club.
"Since I was very young, it's always been a dream for me to play in the Premier League
The style of football played here is similar to the way I play, so it's a dream come true.
"Now I just want to start playing and to start scoring goals."
Southampton have not disclosed the fee paid to Malaga but reports in Spain have suggested the figure is around Â£5million.
The Coin-born player has made one appearance for the senior Spain national team, starting against Holland at the Amsterdam Arena in March.
Saints director of football Les Reed admits the club had their forthcoming Europa League campaign in mind when choosing to recruit him.
He said: "Juanmi is a young, exciting and attacking player who fits into the club's strategic plan perfectly.
"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.
"To have attracted a player of his potential at this early stage of the summer is testament to our determination to build upon the achievements of the 2014-15 season and to continue to implement our long-term plan for the future.
"We will fully embrace the challenge of the Europa League in the coming campaign, and want to develop further in Europe over the seasons to follow.
"Juanmi's arrival is an important step in this process."
Source : PA