Raith, who will begin life in Division Two next term, have also managed to negotiate a 15% sell-on clause for the Spaniard, who scored 20 goals for the relegated Kirkcaldy club.
Novo, who arrived in Scotland from Spanish club Huesca, proved a huge hit with the Rovers fans in an otherwise wretched season.
"Everyone at Stark's Park is sad that the wee man will not be with us for the coming campaign," said a Raith spokesman.
"But we could not stand in his way when the chance of proving himself at a higher level came his way."
Meanwhile, Dundee goalkeeper Julian Speroni has agreed a new three-year deal with the club.
The 23-year-old Argentine forced his way into the first team at Dens Park last season and turned in a number of impressive displays.