United were beaten 3-1 in the second leg in France to lose the qualifying tie 4-2 on aggregate to the two-time Champions League finalists.
Lieke Martens scored a 17th-minute opener for PSG but United midfielder Lisa Naalsund brought the tie level in the 47th minute at the Parc des Princes.
But just a minute later the home side were back in front as Martens scored her second, before Sandy Baltimore gave the French side a two-goal advantage to end United’s hopes of reaching the group stages.
Marc Skinner’s side’s defeat means the only British team in the Champions League group stages are Women’s Super League champions Chelsea.
Arsenal suffered a shock exit in the first round of qualifying after they were defeated on penalties by French side Paris FC.
Scottish Women’s Premier League champions Glasgow City fell at the same stage as United as they suffered a second-round qualifying defeat to Norwegian champions Brann following a 6-0 aggregate loss on Wednesday.
SWPL runners-up Celtic had been knocked out in the first round of qualifying with a penalty shootout defeat to Norwegian side Valerenga.
The hosts started strongly and looked like taking the lead after 10 minutes when Tabitha Chawinga, goalscorer in the first leg, rounded Mary Earps but shot tamely and Maya Le Tissier cleared.
The opener came eight minutes later. This time Earps did well to deny Chawinga but could do little as Martens pounced on the rebound and curled past the United ‘keeper.
United tried to reply quickly with Geyse teeing up Naalsund in the box but the Norwegian could not take the chance and the visitors had a let-off when Martens headed over.
Skinner’s team went close before the break when Geyse combined with Ella Toone but the England international failed to make clean contact and pulled her shot wide.
United did get themselves back into the game soon after the restart when Geyse again found space and Naalsund was on hand to turn home from in front of goal.
Yet it was to prove a short-lived response as PSG quickly went up the other end and regained the lead.
Martens again did the damage, grabbing her second from close range following more good work by Chawinga.
United searched for a second equaliser but Katarzyna Kiedrzynek saved from Hannah Blundell and Geyse.
PSG took a firm grip on the tie just before the hour as winger Baltimore outran Blundell and chipped Earps from a tight angle.
Still United fought on and Katie Zelem drew another save from Kiedrzynek from a free-kick.
Leah Galton then headed the ball into the net but the effort was ruled out for a soft foul on Kiedrzynek, who required treatment after colliding with the United player.
Toone struck the post with a spectacular effort in stoppage time but it was not United’s night.
Manchester United return to WSL action on Sunday as they face Everton away at Walton Hall Park; kick-off 1pm.
