Jol signed Stekelenburg for £4.8million on a four-year deal from Roma in the summer, where he had spent two years after earlier making his name at Ajax.
But the Holland international picked up a shoulder injury in the opening day of the season win at Sunderland and was forced off late in the game.
David Stockdale deputised in his absence but Stekelenburg came back into the side for the latest 4-1 win at Crystal Palace.
Jol told the Fulham & Hammersmith Chronicle: "Maarten came to us and we paid more money for him than for other players, beside Bryan Ruiz a couple of years ago.
"I didn't buy him to be on the bench, you know what I mean?
"He did very well when he started, saved a couple of points against Sunderland.
"Stockdale did well, but Maarten was fit for the last two weeks and showed that he was fit and that he could play again.
"I asked him if he could play and he said 'yes'. I had a little word with Stockdale and of course he isn't pleased but that is the decision I made."