Laurent Blanc's side closed the gap to leaders Marseille - who play Lyon on Sunday - courtesy of a comprehensive victory at the Parc des Princes.
In a game that saw both sides finish with 10 men thanks to the first-half dismissals of Gregory van der Wiel and Andre Biyogo Poko, PSG gained control through Lucas Moura goals scored either side of the interval - the first a penalty on the stroke of half-time.
Ezequiel Lavezzi added a third nine minutes from time but the damage was done, with PSG now four points off Marseille, and Sagnol felt his lengthy injury list and the timing of Lucas' opener were critical.
"Today it hurts. There are some surprising match facts but Paris deserve their victory. They had much better control than us and were better going forward," said Sagnol who was without a host of first-teamers including Ludovic Sane, Henri Saivet and Jussie.
"Psychologically, the [timing of the penalty] played a part. With a full complement we can maintain third place. There were five or six major players who are not here."
Bordeaux ended the day in fourth after Nantes extended their unbeaten run in the league to six matches with a 2-0 win over Evian.
Jordan Veretout and Yacine Bammou scored in either half to continue Nantes' fine run while Caen picked up a big win against north-western rivals Lorient.
Goals from Lenny Nangis and Mathieu Duhamel were enough to gain Caen a first home win of their Ligue 1 campaign while also moving them out of the relegation zone.
Monaco saw off a spirited effort from Bastia to run out 3-1 winners at the Stade Armand Cesari after Christopher Maboulou had cancelled out Valere Germain's opener.
Late goals from Geoffrey Kondogbia and Yannick Ferreira Carrasco ensured maximum points for the visitors while at the Stade Auguste-Delaune II, Benjamim Moukandjo left it late to secure the points for Reims.
As was the case with his first league goals of the campaign, against Lorient last month, Moukandjo struck in the final stages to ensure victory - Montpellier the victims of Moukandjo's late show on this occasion.
