Having already fallen behind in the race to secure a top-three spot in the league, City's hopes for silverware and a positive end to the campaign were resting purely on success in the FA Cup.
But with more key players ruled out through injury during the international break – Vivianne Miedema and Jill Roord both picked up issues with the Netherlands – it was always going to be tough.
Interim manager Nick Cushing's side were put under pressure immediately by United as the visitors pressed intensely and tested City's defence with direct balls over the top.
Jayde Riviere constantly found Bizet down the right-hand side and England international Toone dominated midfield.
It was Toone's searching ball in behind that picked out Bizet early on and she coolly curled it into the far corner past goalkeeper Keating.
City had barely settled before Clinton made it 2-0 when she was allowed to move through the box completely unmarked to head Gabby George's corner in.
There was a response from City but only after striker Mary Fowler was forced off with a knee injury and Cushing had to move players out of position to accommodate with an already-thin bench.
Kerolin stepped up to the plate, causing havoc for United's defence, but could not beat Tullis-Joyce with an acrobatic volley and had other efforts blocked by centre-backs Maya le Tissier and Millie Turner.
At the other end, City goalkeeper Keating was kept busy as Toone and Bizet came close to extending United's lead.
The depleted squad left few options for Cushing off the bench and even though United took their foot off the gas a little in the second half, City did not have enough to fight their way back into it.
"My message this week will be to go and perform for our fans. We need to strip it back to basics," said City interim boss Cushing.
"We have to show more desire. This team is a winning team and we have to make sure every person and process is focused around the direction of winning.
"At the moment, we're in a position we shouldn't be in."
While City's summer is set for a rebuild – they must reflect on a poor campaign, find a way to close the gap on title rivals Chelsea and recruit a permanent manager – United's could end in trophy success.
England midfielder Clinton spent last season on loan at Tottenham and had to miss the final, in which they lost to her parent club United, but she now has a chance to play in the showpiece, alongside best friend and team-mate Bizet, who was also in the Spurs squad last year.
It was fitting their names were on the scoresheet at Joie Stadium.