With 12 minutes left Giuseppe Sannino was threatening to go down as one of the FA Cup's great folk heroes by leading Watford to a classic giantkilling act.

That was until Sergio Agüero popped up to collect his second of the tie to level the scores at 2-2 before what was to be true heartbreak for the travelling support. With five minutes remaining Aleksandar Kolarov took aim from outside the area and hit the attempt straight at Jonathan Bond, only for the ball to squirm under the goalkeeper and into the net. In that moment the dreams of Watford, a 40-1 shot and 16th in the Championship, were shattered.

Worse was to follow for Bond who, deep in added time, flapped at a cross to allow Agüero to secure his hat-trick goal – his 25th in 24 appearances this season.

For Manuel Pellegrini this was a scare he could have done without. "I was very worried," the Chilean said. "I talked to players before the match – here in the FA Cup, the Spanish Cup, Italian Cup, teams from lower divisions have a lot of motivation. If you don't play with intensity or 100% concentration, then you will not win the game. What Watford did in the first 45 minutes – and we were jogging – that way it was impossible to win.

"If I could change 11 players [at half-time] I would change all of them. It was more the thing of attitude and intensity than individual players. The whole team did not do things we normally do. The most important thing was Watford did not score the third goal. If Watford score the third goal the game was finished. We defended very bad in the first half."

Pellegrini could take succour from the way his side responded in the second half. "They have a very good reaction and we played with another tempo and another pace, we played like we did in the whole season here."

Tempers had frayed early on when Edin Dzeko squared up to Gabriele Angella and received the game's first yellow card. This occurred as Jesús Navas waited to take a free-kick after Micah Richards had been yanked down, which came to nothing.

It was Angella who upended Richards to give away another free-kick from which Watford broke and nearly scored. Slick work between Marcos Lopes, Agüero and Navas moved the ball to Yaya Touré. But when the Ivorian unloaded his cannon of a right foot, the rebound allowed the visitors to counterattack. Fernando Forestieri was released into space and ran at the backpedalling Martín Demichelis but when the forward tried to square the ball, it was overhit and Costel Pantilimon gathered.

This proved an unheeded warning, as Watford took the lead. Demichelis was again made to look flat-footed when Cristian Battocchio pinged in a pass to Troy Deeney and, as the centre-back went to close the striker down, the latter planted the ball around the corner to put Forestieri through on goal. This time the 24-year-old made no mistake.

Demichelis's afternoon got worse. A clumsy ball by the pony-tailed Argentinian was intercepted by Sean Murray. He found the seemingly omnipresent Forestieri and when the ball was moved on to Deeney, he buried the chance.

Despite missing David Silva, Samir Nasri, Álvaro Negredo, Pablo Zabaleta, Vincent Kompany, Joe Hart and Fernandinho from Pellegrini's strongest XI, there was still no excuse for the disjointedness. When the manager sent his team out following a stern word at the interval, Zabaleta and Kompany had replaced Richards and Jack Rodwell – as a precaution after their return from injury – with Pellegrini pushing Demichelis alongside Touré in midfield, rather than bringing on Fernandinho.

Agüero's first goal came when Kolarov drove a cross over from the left, Dzeko's stabbed attempt was blocked by Bond, and City's No16 calmly slotted home. Before the Argentinian's intervention this was being written up as a triumph for Sannino, a former hospital cleaner who – having not coached at the top level until he was 54, three years ago – was the man to mastermind the end of Manchester City's quadruple dream.

Instead, he will have a job consoling Bond, who trudged off the turf looking distraught. Sannino said: "He's OK and you have to keep in this mind on this day not [the] mistake – he was very good.

"I told my players to enjoy it and be free on the pitch. I want to compliment the players for their desire and they kept the composure. I feel a bit bitter because at 2-2 we were still in the game and could have played a different way towards the end."

Yet Sannino and his players should feel proud – far better teams have come here and failed to lead City by two.