Having secured top spot in Group F ahead of their final match in the section, Martinez took the opportunity to rest a number of key players, with Joao Cancelo, Bruno Fernandes, Ruben Dias, Bernardo Silva, Pepe and Vitinha among those to drop out of the team.
Portugal had their moments during Wednesday's clash, but Georgia recorded a 2-0 victory to book their spot in the last-16 stage of the competition.
The breakthrough came in just the second minute of the contest, with Khvicha Kvaratskhelia finding the bottom corner following a mistake from Antonio Silva high up the field.
In-demand Benfica centre-back Silva then conceded a penalty in the second period, which Georges Mikautadze dispatched, to secure a two-goal victory for Willy Sagnol's side.
Martinez admits Portugal were below-par against Georgia
Martinez had no qualms over the final result on Wednesday, with the Spaniard insisting that it was necessary to make changes to his side ahead of their last-16 clash.
"We made a lot of changes. The focus was on preparing all the players," Martinez told reporters after the surprise defeat. "Now we are more prepared.
"We had players on the bench today that we did not want to use, because we were first in the group and the goal was achieved.
"It's a difficult way to prepare for the next game, because we don't like to lose. It's the first official game we've lost. But we're ready now.
Portugal will face Slovenia in the round of 16
"We weren't clear-headed enough with the last pass and in front of goal, and their goalkeeper had an amazing performance. We tried to score but couldn't and that made Georgia believe all the more. They deserved to win.
"It was a day when we didn't have the same intensity as the opponent. For Georgia, this was a final; for us, it was one step before the round of 16. That was part of the final result."
Portugal's reward for topping Group F is a clash with Slovenia in the last-16 stage of the competition on Monday night.
Martinez will recall his key players for the battle against Slovenia, who drew all three of their matches in Group C to qualify as one of the best third-placed outfits.
Cristiano Ronaldo once again started at the tip of the Portugal attack on Wednesday, but the Al-Nassr forward found it difficult to make his mark, and Martinez now faces a big decision over his involvement in Monday's contest.