It looked like Nuno's side would be frustrated by a superb goalkeeping display by Slovan Bratislava's Dominik Greif, who included a Ruben Neves penalty save at the start of the second half among his heroics.
However, his resistance was finally broken by Jimenez's towering header in injury time from Adama Traore's cross to give Wolves a 1-0 win at Molineux.
They now need just a point to progress to the knockout stage in the new year as they are second in Group K with nine points, five ahead of Bratislava in third with just two games left.
Jimenez's goal came in the second of 12 minutes of injury time, following a long period of treatment for Bratislava's Kenan Bajric, who suffered concussion after being caught by the Wolves forward.
Nuno felt his side deserved the win but admitted it had been a difficult evening as they failed to convert their chances.
"We had to be patient but I thought we played well and created a lot of chances," he said.
"We combined well and dominated against a good team, they are an organised team. If you allow space to them then it is difficult. Good team and good players and a good coach.
"It took time but it was a fantastic moment for the team. We were pushed on by Molineux so it was good for everyone."
Wanderers now switch focus back to the Premier League and Sunday's West Midlands derby against Aston Villa.
Dean Smith's side visit Molineux for the eagerly-awaited fixture with Wolves 12th and Villa 16th in the table, although only two points separate the local rivals going into the weekend's action.