The France international had appeared to have his move to Lyon all but finalised, agreeing to join the Ligue 1 club on loan with an option to buy at the end of the season. However, Lyon were unable to register the deal before the French transfer window shut at 20:00 BST, leaving the 27-year-old midfielder without a club just hours before the Spanish deadline.
Sevilla moved quickly to take advantage of the situation, negotiating directly with AC Milan to sign Fofana on loan without an option to buy.
The Andalusian club had believed their business for the window was largely complete after earlier bringing in forward Lucas Stassin and winger Felix Correia, but sporting director Jose Ignacio Navarro identified the late opportunity and acted decisively to strengthen a midfield head coach Luis Garcia Plaza had publicly identified as needing reinforcement.
Fofana joined AC Milan from Monaco in 2024 and has struggled for game time this season, left out of preseason friendlies and training separately from the rest of Sergio Conceicao's squad. He had also been linked with Besiktas and Galatasaray earlier in the window, along with Real Betis, though talks with the Seville rivals never advanced into a concrete offer.
The move gives Sevilla a 27-man squad and a fresh option in central midfield, an area the club had identified as the position most in need of reinforcement heading into the new campaign. Fofana, capped by France at senior level and a member of their squad at Euro 2024, arrives with considerably more top-level experience than much of Sevilla's existing options in that area of the pitch.
The final negotiations were reportedly unblocked in a direct conversation between Navarro and Milan director Hendrik Almstadt, who agreed terms allowing Fofana to move on loan despite the Italian club's initial financial demands proving difficult for Sevilla to meet.
For Fofana, the switch represents a considerable change of scenery after two seasons in Serie A, and a chance to reboot his career in LaLiga having fallen out of favour in Milan. Whether the move becomes anything more than a season-long stopgap will likely depend on how he performs under Garcia Plaza between now and the end of the campaign.