McIntyre crossed for a try and added 11 points from the tee as the Catalans won for the first time in eight games, a run dating back to November.
The Parisians missed out on the chance to go top above Toulouse as they lost for the first time in five league matches.
McIntyre found a way over after just 11 minutes before winger George Tilsley crossed to give Perpignan a three-point half-time lead after Jeremy Ward's score for Stade Francais.
Tries from Samoa lock Piula Fa'asalele and compatriot Genesis Pelepele Lemalu before the hour mark put Perpignan in control.
Winger Lester Etien touched down to give Stade hope and Tilsley was sent off for a stamp on Morgan Parra with 12 minutes remaining.
Sione Tui's try cut the gap to seven points in the 73rd minute but Perpignan held on.
Earlier, Fiji centre Josua Tuisova crossed as Lyon beat Clermont 34-14 at home, handing Christophe Urios a defeat in his first game in charge of the visitors.
Former Olympic champion Tuisova was at his bulldozing best and was rewarded for his efforts with a minute left as he claimed his fifth try of the season.
Sebastien Taofifenua, Tavite Veredamu, Patrick Sobela were the other try-scorers for sixth-placed Lyon.
Urios, who left his job as Bordeaux-Begles head coach in November, took over from the sacked Jono Gibbes earlier this month with the two-time champions in 10th place.
Samoa No. 8 Fritz Lee scored the only try for Clermont, who have just one win in seven games in all competitions and remain six points above the relegation play-off place.
Elsewhere, Argentina back-rower Facundo Isa scored twice as Toulon, without Wales fly-half Dan Biggar who is preparing for the Six Nations, overcame Pau 27-16.
On Sunday, league leaders Toulouse welcome Montpellier without eight players away with France's Six Nations squad including influential half-backs Antoine Dupont and Romain Ntamack.
The games end a tumultuous week off the field in French rugby after national federation president Bernard Laporte resigned following his conviction of corruption in December.
