Musicians left the stage and the audience was asked to leave the concert hall.
Marc Reinhardt, a spokesman for Lucerne University of Applied Sciences and Arts, whose students were performing, told the Associated Press an audience member tried to save Yinon, but he died in the ambulance on his way to a hospital.
He had no details on what led the conductor to collapse and it is not yet known what caused his death.
The theme of the concert was 'the healing Alps' which, as various Swiss media noted, was a cruel irony given how events unfolded.
Yinon had previously conducted the BBC Symphony and Berlin Symphony orchestras, and various others across Europe, making numerous CD recordings.
He was initially trained in Tel Aviv and Jerusalem.
Yinon had previously led the students of the Jungen Philharmonie Zentralschweiz orchestra in concerts in 2009 and 2012.
The school said they lost 'not only a highly regarded musical colleague and sensitive educator, but a big-hearted friend.'