The match, a Turkish Cup semi-final second leg at Fenerbahce's ground, was abandoned in the 57th minute after the incident with the score at 0-0 on the night and 2-2 on aggregate.
Turkish television pictures showed Gunes clutching his head in pain and bewilderment and falling to the turf after being hit by the projectile, suspected to be a cigarette lighter.
At least 15 Fenerbahce fans were arrested as police made their way into the stands to find offenders, according to local reports. Besiktas boss Gunes was hit on the head by an unidentified object and reportedly needed five stitches and his assistant, Erdinc Gultekin, was left with a bloodied face after a furious tunnel bust-up between both sets of players and staff from the Istanbul rivals.More news: Mickey Mantle Baseball Card From 1952 Sells for $2.88 Million
Here is the unfortunate Gunes after receiving treatment, which included a number of stitches, in hospital.
The stadium was heated up more when in the 58th minute of the game, an argument ensued between Besiktas goalkeeper on the bench and several Fenerbahce fans.
Besiktas chairman Fikret Orman called it a "sad day", while the Turkish Football Federation said it would make a decision on the match in the "coming weeks".More news: Robert De Niro hits out at Trump at Tribeca Film Festival
The match had already been halted for five minutes in the first half when projectiles where thrown at Besiktas players.
One of the great purveyors of shithousing in world football, Portuguese hardman Pepe was at it again on Thursday with Besiktas, sent off after a shocking challenge.
The derby between Istanbul football giants Fenerbahce and Besiktas has been abandoned by the referee after the visiting manager got injured by objects flung from the stands.More news: NFL Schedule: Eagles and Falcons to Open Season