The Cottagers handed the initiative to their hosts early on and never really retrieved it, with Steven Pienaar netting a 16th-minute strike which turned out to be the winner.
Jol concedes his side did not deserve to take much from the encounter but feels they improved in the second half.
"We didn't deserve a lot, they were the better team," he told Sky Sports.
"It's 1-0 and when it's 1-0 in an away game you always feel you could have had a bit more. But it could have been two or three (to Everton) as well so I can't complain.
"The second half was a bit better but the first half was lacking."
Jol was frustrated to see some of Everton's players go unpunished for challenges on members of his side.
He added: "The challenges on Urby (Emanuelson), (Alex) Kacaniklic and (Giorgos) Karagounis, the referee said 'no, it was nothing'.
"We've had a few red cards for these challenges. But that was only frustration."
Jol had to replace Dimitar Berbatov after just 30 minutes because of injury but he said it was too early to say whether the Bulgarian would miss the remainder of the campaign.
Asked whether he had ruled out the striker for the final three games of the season, Jol added: "Berbatov has got a tear in his calf. He normally says he is a quick healer so hopefully not."