The American opened the scoring after 30 minutes with a long-range free kick before doubling his tally just before half-time with a simple header.
With other strikers out injured, such as Pavel Pogrebnyak, Jol was delighted that the 29-year-old stepped up to steal the show at the Reebok Stadium.
“He will always be at the end of things, of crosses, like he did with the second goal,” Jol told reporters.
“[Pogrebnyak] was not there, Andy Johnson was not there, so he was the only solution for us.
“If you consider that he’s scored most of his goals from a wide position then it’s quite amazing.”
Dempsey’s goal now leaves him on 15 in the league this season - the highest total for a Fulham player in their Premier League history - but the former Tottenham boss highlighted other crucial performances in their victory.
He added: “I’m pleased with all the guys. We looked dangerous with Duff in the first part of the game then we scored with a free-kick.
“Very good attacking with the second goal, and especially the second half was pleasing because normally if we get under pressure we tend to play in a different style.”
The Cottagers sit 10th after the win, and although they cannot qualify for continental football, Jol believes his players can build on their back-to-back wins to help foster a winning mentality.
“Our aspiration is to play good football because you can’t say that we play for Europe,” he added.
“The only thing is trying to create a winning mentality and to get as many points as possible, and that won’t be easy as this was - though it is simple to say - probably our easiest game of the games we still have to play."
Meanwhile Bolton boss Owen Coyle was not pleased with some of the defensive marking by his side.
“Yeah, I don’t think there’s any doubt about that,” Coyle said when asked if the home defeat was disappointing.
“Coming into the game, and being at home, we were looking to make it four wins on the bounce. I thought the game, to be fair, was an even start, there wasn’t a lot in it.
“The second goal [was] right on the stroke of half time, we’ve given it away. It was a poor pass under no pressure and we’ve then been got caught on the counter-attack.
“Clint Dempsey’s out there, unmarked, with a free header, so it’s certainly hard to take.”
The loss leaves Bolton hovering tentatively at 16th in the table and Coyle feels it is an opportunity missed for the Trotters to push away from their fellow relegation-threatened clubs.
He added: “We certainly came into the game trying to win and I think the way a couple of results went today it was a chance to open up a gap.
“It’s certainly disappointing. The first goal I always feel in the Premier League is vital and that really turned the game on its head today."