The tiny British Overseas Territory with a population of 29,000 became a full member of UEFA earlier this year despite opposition from Spain, which claims sovereignty over Gibraltar.
UEFA's executive committee has reviewed the procedure for the draw on February 23 in Nice and the organisation's general secretary Gianni Infantino has confirmed the two member nations will be kept apart due to the sensitivities involved.
Infantino said following the meeting in Bilbao: "Gibraltar is a full member and will participate in the draw on February 23, but it will not play against Spain. That was one of the criteria that was decided."
UEFA also called for a uniform approach to tackling match-fixing across Europe.
Infantino said: "We want concrete and effective policies to fight against match-fixing, preferably consistent and uniform instead of having one sanction in one country and one in another."
The executive committee gave its support to a draft 11-point resolution on the integrity of football which will now go to UEFA's Congress in March.
UEFA will also push for the International FA Board to reconsider the so-called 'triple punishment' - where a player who denies an opponent a clear goalscoring opportunity in the penalty area is effectively punished three times.
Not only does the player concede a penalty, he or she is also sent off and automatically suspended for the next match.