The champions were without a number of players, but so too were Newcastle in a match that meant so much to them.
In the end, a solitary Titus Bramble goal was all Newcastle required as they booked seventh spot - two points clear of Bolton.
They will now play just one Intertoto tie, probably against opposition from Norway or Iceland with victory guaranteeing a place in the second qualifying round of the UEFA Cup.
Typically of Newcastle they had to do it the hard way, having Stephen Carr red-carded after 75 minutes for a foul on Lassana Diarra and then being forced to repel a non-stop Chelsea tidal wave.
There was a pre-match blow for the Blues when they lost skipper and goalkeeper Carlo Cudicini with an ankle injury in the warm-up, forcing Mourinho to hand a first start to Lenny Pidgeley.
Once again there was no appearance in Newcastle colours for Michael Owen.
The Premier League champions started brightly and posed plenty of problems with a forward line of Damien Duff, Arjen Robben and Joe Cole.
Newcastle eventually took a grip on the game and Emre lashed a 30-yarder just over the bar.
Pidgeley appeared nervous but twice just beat Michael Chopra to throughballs, before hanging on to a Chopra shot on the turn.
There was disaster for Newcastle on the half-hour mark when the inspirational Solano attempted an overhead kick but was caught from behind and had to be stretchered from the pitch with what appeared to be a shin injury.
It was not until the 41st minute that Shay Given was called into action, saving at the second attempt to keep out a low drive from Duff on the break.
A double half-time substitution saw Shaun Wright-Phillips and Carlton Cole replace Duff and Robert Huth and Chelsea upped the gears.
William Gallas had a goal disallowed for offside and Wright-Phillips suffered a similar fate after putting in the rebound when Maniche's shot rebounded out off the post.
The winner arrived after 73 minutes when Amady Faye headed Emre's back post corner across goal and Bramble scored with a ferocious right-footed volley.
The result means United's caretaker boss Glenn Roeder has now won 10 of his 15 games and with 32 points from a possible 45, his record is bettered by only Liverpool and Manchester United.