The match, played behind closed doors, was delayed after the man used a heavy duty lock to secure himself to the posts in protest at Israel’s military operation in Gaza.
The game eventually kicked off 45 minutes later than planned, with Scotland running out 4-1 winners.
Several hundred people, some carrying small coffins and Palestinian flags, had gathered outside the doors of the main stand.
The protester who gained entry to the national stadium was earlier wearing a hi-vis vest, so he may have been mistaken for a steward.
He was cut free from the posts and led from the pitch by police.
Players were seen discussing a second warm-up and whether it was safe to return to the pitch shortly before the match got under way.
The match kicked off to the sound of demonstrators outside booing, blowing whistles and setting off fireworks.
A handful of counter-protesters also demonstrated before the group B2 game.
Last week, the SFA said it had been left with “no option” but to bar supporters from attending “following extensive security consultations with all key parties”.
Public demonstrations against Israel’s military operation in Gaza have been happening regularly across the UK.
One group – the Gaza Genocide Emergency Committee – arranged a protest before the game at Hampden and called for the matches to be cancelled.
Police Scotland said: “Appropriate policing plans are in place to maintain public safety and minimise any disruption to the community.”
Israel was banned from hosting any football matches by UEFA for security reasons in the aftermath of the 7 October attack by Hamas and the Israeli government’s military response.
Instead, the Israeli national side and its club teams have played fixtures at neutral venues in Hungary.
Tuesday’s return game between Scotland and Israel in Budapest will also be played behind closed doors.