The government said it is a "thank you" to individuals and groups involved in Legacy 2014 programmes to promote sporting participation across Scotland before and after the Games.
Some 2.3 million requests were made for up to one million tickets when the application process opened last year. Some of the events at the Games were massively over-subscribed and Glasgow 2014 allocated tickets via a draw.
More than 100,000 applications were made for the 100m men's final at Hampden Park, with track cycling, diving and artistic gymnastics among the other sports over-subscribed.
Around 94% of public tickets have now been sold, organisers said.
Glasgow City Council announced in November that it is to give 6,000 tickets away to children, community groups and over-60s in the city.
Selection will begin in March with successful applicants being told in May.
The latest batch of free tickets will cover a range of events over the 11 days of the Games and they will be allocated through sportscotland, Education Scotland and Big Lottery Fund, which are involved in the legacy programme.
Children involved in school and community sports clubs, coaches and volunteers and people from disadvantaged or disability groups will benefit, the government said.
The scheme was announced by Sport Minister Shona Robison as she visited a Perth primary school for a coaching session with Team Scotland para-athlete Meggan Dawson-Farrell.
Ms Robison said: "This gift of 5,000 Legacy Tickets will recognise the valuable contribution made by people to deliver a meaningful legacy. We're making sure we can say a big 'thank you' whilst offering beneficiaries the chance to see the best in sporting action, or experience the thrill of the opening or closing ceremony, and deliver an "I was there when" moment.
"My hope is that the memories created by seeing the Games will last a lifetime."
Dawson-Farrell, 21, will compete in the wheelchair T54 1,500 metres at the Games in Glasgow.
She said: "This summer will see some of the best athletes that Scotland has to offer, both able-bodied and disabled, representing their country united - cementing the bridge to equal opportunity.
"I wish this for all young people, I believe the Games can help bring this about."