The first leg of the Champions League qualifier at Windsor Park in Belfast was marred by incidents.
Play was held up when a bottle was thrown at Griffiths and there was an attempted pitch invasion at full-time.
Linfield have been charged by Uefa with the "throwing of objects" and a "field invasion".
Scottish champions Celtic have also been charged with "improper conduct of the team" after they picked up more than five bookings.
One of the players booked was Griffiths, who was shown a yellow card by referee Alejandro Hernandez as he picked up a bottle that had been thrown at him while he was taking a corner.
Police with dogs were deployed at full-time to stop a pitch invasion.
European football's governing body Uefa will deal with the case on 20 July, the day after the return leg in Glasgow.
Celtic had decided not to take up an allocation of tickets for the game because of security concerns - but around 300 fans watched.
Speaking after the match, Celtic manager Brendan Rogers said: "Players go onto the field and it should be a safe environment for them. You want the passion from the stands to stay in there - but if you take that away from it, it was a good evening."
Police Scotland released a statement urging fans to remain "focused on the football" during the return leg.
Superintendent Craig Smith said a "robust policing plan" had been put in place following co-operation with the Police Service of Northern Ireland.
He added: "Anyone who is intent in causing disorder or hate crime can expect to be arrested by police."

Dr Antinori has been placed under house arrest and banned from practising pending a police investigation.
The complaint, rejected by the doctor's lawyers, was made by a 24-year-old Spanish woman.
Dr Antinori shot to fame in the 1990s when he helped a woman give birth at 63, a first at the time.
The 70-year-old was arrested at Rome's Fiumicino airport and is now under house arrest in the Italian capital.
According to Italian investigators, the Spanish woman, who was temporarily working at Dr Antinori's Matris clinic in Milan, had her mobile phone taken and was forcibly immobilised and anaesthetised before her eggs were harvested.
Lawyers for Dr Antinori, nicknamed the "grandmothers' obstetrician", said the doctor was an innocent victim of extortion.
Prosecutors believe his may not be an isolated case, according to the Italian media.
Donata Lenzi, an Italian MP, said: "The arrest of Severino Antinori is extremely serious because it indicates the existence of a market in eggs that will not stop at anything."
Dr Antinori became famous worldwide in 1994 when he gave fertility treatment to Rossana Della Corte, an Italian who at the time became the oldest woman to give birth.
He also helped Patricia Rashbrook, who became the UK's oldest mother in 2006.
In 2003, the controversial doctor said Italian authorities were persecuting him over his human cloning projects.
This followed his announcement that one of his patients would give birth to a cloned baby.
Celtic striker Leigh Griffiths has been charged with "provoking spectators" after he tied a scarf to the goal following Friday's 2-0 win at Linfield.
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Well-known Italian fertility doctor Severino Antinori has been arrested after a woman said he had forcibly removed eggs from her at his clinic.