Midfielder Michael Lang tucked in an 89th victor for Basel after Raoul Petretta found him with a pinpoint low cross at the far post, giving United's stand-in keeper Sergio Romero no chance.
Manchester City opened up an eight-point lead over United while Pogba was convalescing, but both he and Ibrahimovic spoke optimistically about reeling in Pep Guardiola's side after Saturday's game.
Mourinho will be especially frustrated by the defeat because it means he can not afford to rest players against CSKA, just days before the Manchester derby.
Marcos Rojo may also be recalled after fully recovering from a knee problem of his own, while Paul Pogba could be rested as he builds towards achieving full match sharpness.
"I believe that with the minutes going probably my players felt we didn't score until now, we don't concede and we get the point and in the last minute they score".
"We were in an easy way for many periods - it looked nearly impossible not to win".
Mourinho had expressed concern about the pitch at St Jakob-Park after it was replaced following heavy damage during Switzerland's recent World Cup play-off with Northern Ireland. Paul Pogba played 66 minutes.
Lang hit the bar with a header after besting Daley Blind aerially before United's defence scrambled clear.
But after watching his side waste a series of chances in front of goal during the first half of Wednesday's encounter, with the likes of Romelu Lukaku, Anthony Martial and Mauroane Fellaini all coming close for the side, Mourinho was left to reflect on what could have been.
Martial was denied by Vaclik at the end of a surging run before Rojo rattled the bar from long-range.
"We were not informed, apart from that I don't have to speak with Southgate, I just wish [for the] good and want him to be successful".
Suddenly unable to find any rhythm, United rode their luck again as Renato Steffen's powerful effort was narrowly off-target.
Mourinho threw on Marcus Rashford and Zlatan Ibrahimovic but the attacking duo had little impact.
And, in the 89th minute, Basel's Raoul Petretta fizzed a low cross across the box for Lang to tap in at the far post.
The allegation was made just a day after the Old Vic released results of its own internal investigation into the matter. The Old Vic apologised "for not creating an environment or culture where people felt able to speak freely".
Morrissey has come out to defend Harvey Weinstein and Kevin Spacey in a recent interview and people are not very happy about it. He was wondering where the boy's parents were. "One wonders if the boy did not know what would happen", Morrissey said .
Instead of a map, this expansion brings a new event called Breakout, but there will be two operators. Season 2 is taking place in a new location in Italy and will feature two new Italian GIS operators.
The ARA San Juan submarine shown here has been missing for two days after giving its last location in southern Argentine waters. Argentina's navy is analysing a noise that may have come from a missing submarine with 44 crew members on board.
He leveled in the eighth game before breaking once more in the 12th to snatch the set, despite Goffin hitting eight more winners. At 3-0 in the second set, Goffin was digging his heels into the game. "This has always been, again, a dream of mine".
He later wrote: "Shoplifting is a very big deal in China, as it should be (5-10 years in jail), but not to father LaVar". All three UCLA players have been indefinitely suspended from the team, coach Steve Alford said.
Saudi Arabia has since 2015 been leading an Arab coalition fighting on the side of Yemen's internationally recognized government. His son-in-law and adviser Jared Kushner has reportedly formed a bond with Saudi Crown Prince Mohammed bin Salman.
Ashes: All eyes on sore Warner and Shaun Marsh
England have named their XI, which includes seamer Jake Ball ahead of Craig Overton who's performed well in warm up matches. He even joked that Warner might even adopt West Indies legend Shivnarine Chanderpaul 's unusual stance if need be.
Three Pakistani LeT terrorist killed in Jammu and Kashmir
However, when security forces were moving towards a particular area, militants hiding there, fired at them with automatic weapons. His elder brother Musaib was killed in an encounter in the Hajin area of Bandipora district in January this year.
Mastermind Hafiz Saeed to be Released From House Detention
The government had informed the judicial body that Saeed's release could lead to imposition of worldwide sanctions on Pakistan. A Punjab Home Department official said it is feared the release could invite global sanctions on the country.
What Does Net Neutrality Rollback Mean For You?
Language in the new proposal would give the FCC significantly less authority to oversee the web. Those who criticize the rules say undoing them is good for investment in broadband networks.
Zanu-PF: The Mugabe heave-ho will start tomorrow
"I hope that 37 years into [his] rule he doesn't want another 37 seconds of rule", said war veterans' leader Chris Mutsvangwa. But she is insulting civil servants, the vice president, at public rallies.
Adoption makes a big difference in a child's life
State authorities removed Ireland from his home when he was 3, and Quinn said she immediately wanted to care for him herself. Phillips said Adoption Day is meant to promote adoption as an option for families who want to help kids find permanency.
Country music legend Mel Tillis dead at 85
In 2011, Tillis was named a National Medal of Arts recipient for his contributions to country music, the Tennessean reported. He also briefly co-hosted an ABC prime-time series, " Mel and Susan Together", with supermodel Susan Anton in 1978.