Goals from Steven Defour and Kevin Mirallas were enough to send Gordon Strachan's side to a second successive loss and, coupled with Macedonia's win over Wales, left them at the foot of the table with just two games to go.
Whittaker, though, felt that Scotland had put in another strong display against a side considered to be among the best in the world and was confident they would continue to build on that momentum when they face Macedonia on Tuesday.
"We are pretty gutted in the changing room," said the Norwich City defender. "We put a lot into the game but they were clinical when they got their chances and that was the difference. It was tough but there were spells where we played some quite nice stuff but it never really came off. The manager has said we have to stress the positives of the performance rather than dwell on the defeat. He has brought a freshness and a positivity. It shows on the pitch because we are all in it together. Hopefully, results will start to match the performances soon."
Whittaker was frustrated at his role in Belgium's first goal, the defender conceding possession to Marouane Fellaini. Two passes later and Steven Defour was putting his country in front. "I got caught a little bit in between and I ended up giving it to Fellaini and further down the line there was a cross and a goal," he said. "That is what you are up against - there are other times where you would get away with it. [But] they have world-class players."
Scotland had a chance to take the lead just before Defour scored when Scott Brown's shot whistled wide. Jordan Rhodes wondered what might have been. "If Scott scores then it might have been a different game," said the striker who came on for Leigh Griffiths in the second half. "It was a case of getting the first goal and unfortunately we didn't. But I can't remember David Marshall having too much to do.
The result leaves Belgium on the cusp of qualifying for next summer's finals in Brazil and Rhodes believes they will be among the favourites. "They won't be going in there as underdogs. Everyone will be very aware of the threat they can pose," he added.