Glasgow fly-half Parks takes the place of Chris Paterson, who started at number 10 in the warm-up games against Ireland and South Africa last month but is named on the bench for the Portuguese.
Murray, Scotland's record cap-holder, resumes his second-row partnership with Nathan Hines, with James Hamilton standing down.
Hamilton, who also started both warm-up games, does not make the bench, with Scott MacLeod the cover at lock.
Marcus Di Rollo comes in for the injured Andrew Henderson (dead leg) at centre, while Scott Lawson and Allan Jacobsen are preferred to Ross Ford and Gavin Kerr at hooker and prop respectively.
Otherwise, it is a very strong team put out by coach Frank Hadden, with flanker Jason White as captain and Simon Taylor and Allister Hogg elsewhere in the back row.
Hadden is happy to have Parks back in the team.
"Dan has trained very well and is playing very well," he said. "When we discussed the selection, we all agreed instantly and came to the conclusion that this is where we want to go in this match."
As for the other experimental selections, Hadden added: "Obviously, we have a few weeks ahead of us and we want to get a balance right with this game, while keeping the squad on their toes.
"We wanted to get the balance and selection as good as possible. We are not just here to give opportunities to players. It's about trying to find the balance.
"The gloves are off. We want to win the match."
Scotland are expected to comfortably see off Portugal, who are making their debut in the tournament.
But Hadden said: "We are respectful of the progress Portugal have made.
"It's very important we start the game well. We are used to being the underdog."