Boss Nuno Espirito Santo dismissed suggestions Wolves are on the brink of reaching Europe for the first time in 39 years.
Andre Gray levelled in the second half, but Ben Foster's error, after he misjudged Ruben Neves' cross, allowed Jota to win it.
Wolves, who have not played in Europe since 1980, are now four points clear of Watford and Everton in seventh, with Leicester, who play Arsenal on Sunday, six points behind.
If the Hornets lose to favourites Manchester City in next month's FA Cup final, seventh in the Premier League will yield a Europa League qualifying spot, but Nuno refused to take anything for granted.
He said: "The final of the FA Cup still has to be played, so why should we be worried about anything else? It was never our aim to compete in Europe.
"Competing in the Premier League is very hard, we must know were we came from. Last season we were playing against Burton, with all my respects, and now we are here.
"We have achieved staying in the Premier League – no-one has said that – and now we are going to be in the top half. Last season we were in the Championship.
"We are not thinking about it. It (seventh) doesn't guarantee anything. We have to prepare for the final game at Molineux (against Fulham)."
Jimenez opened the scoring when he headed in his 17th goal of the season from Jota's cross four minutes before the break.
Watford levelled soon after the break when Gray pounced, drilling in a loose ball after Ryan Bennett's poor backpass gifted Gerard Deulofeu a chance.
But Jota volleyed in the winner when Foster went AWOL coming out to claim Neves' deep centre with 13 minutes left.
"I'm disappointed and sad – we wanted to get a better result, but it was impossible," said Hornets boss Javi Gracia.
"In all the games, whenever we have conceded goals, there have always been mistakes, but in the last few games we have been conceding avoidable goals."
"Before the game, we knew our target was to try and play in Europe – and at this moment, it is the same.
"We have two chances – if we are not able to achieve seventh position, the other way to Europe is to try and win the cup final."
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