Arsenal made a move for the 20-year-old starlet but decided against matching the £37.2 million release clause for the playmaker meaning the high-profile transfer was blockedArsenal target Julian Draxler in the long-term.
Tonnies, who is chairman of the Schalke supervisory board was speaking at SpoBis, a sports business conference in Dusseldorf where he discussed Draxler's future.
The 20-year-old was the subject of a late bid from the Gunners after a delegation was sent to Germany to negotiate a big-money move for the playmaker, however the Bundesliga club rejected the offer.
According to SID Tonnies said: "We cannot keep a super talent like Julian forever. But it also wouldn't be fair to refuse players to jump on the train that is waiting for them.
"We are often talking. I told him he should stay with us another two, three years and that a move would be too early for him now."
Tonnies also moved to alleviate concerns that the starlet could move to runaway Bundesliga leaders Bayern Munich, adding: "He won't go to Bayern, I know that."