Media in Spain had claimed that the two clubs had agreed a €60 million (£51m/$67m) deal for the 21-year-old, who has scored 26 goals in 44 appearances across all competitions this season.
Bobic, who said last month that a deal with Madrid is a "real possibility", has forcefully denied the most recent claims of a completed deal insisting there have been no discussions.
"There has been no contact with Real Madrid," Bobic told ESPN FC. "For once, I don't have to use a white lie, they really haven't been in touch yet. I know them very well."
Jovic has enjoyed a breakout campaign for Frankfurt this season, his second at the club after arriving on loan from Benfica last term.
The reigning DFB-Pokal champions sit in fourth on 54 points and could extend their advantage to five points to fifth place with a victory over Bayer Leverkusen on Sunday with two matchdays remaining.
Frankfurt could also secure Champions League football next season by winning the Europa League – a feat still possible thanks to Jovic's nine goals in the competition this year helping them to reach the semi-finals.
The Serbia striker's goalscoring prowess this season has seen Frankfurt make his loan from Benfica permanent in April, but also had his name linked to many of Europe's top clubs.