The Hibernian midfielder gave his manager Tony Mowbray a fright at Motherwell on Saturday when he took a knock on the same knee which kept him out for most of last season with cruciate ligament damage.
It was déjà vu for his close friend Whittaker, who also watched his team-mate stretchered off on the same ground for the Scotland Under-21 side recently.
But the full-back was relieved to learn the influential Thomson will be fit for tomorrow night. "At first I saw him hold his knee so I feared the worst," recalled Whittaker. "But he was on the bench after half-time. I went over to see how he was and he said it wasn't as bad as he first thought. I was pleased in that respect.
"When he first got into the team he never really got dropped. He got his chance under Bobby [Williamson], took it and had a great season. He was just unlucky to get such a bad injury.
"He missed playing but now he's back, he realises he's been lucky and is enjoying being back in. Since returning to the team, he has gotten better and better with every game.
"He's come on and brought a different look to the team because he's such a great player. He gets on the ball, he's composed with it and he can pick great passes so it's good he's back for Thursday."
Hibernian have their eyes on a place in the group stages after a goalless draw with the Ukraine outfit at Easter Road.
While Dnipro drew yet another blank, in a 0-0 draw with Chornomorets on Sunday, the Edinburgh side warmed up with an impressive 3-1 win at Fir Park.
The third-placed Scottish Premier League side have hit the net 14 times in eight matches - including a 3-0 win at Ibrox - and Whittaker is confident of more goals. "We can definitely score," the 21-year-old said.
"We've got dangerous players such as Derek Riordan, Ivan Sproule and Garry O'Connor all scoring and even Michael Stewart from midfield at the weekend. They are all forward-thinking players for us. There is very rarely a game goes by that we don't score."
Whittaker revealed some of his manager Mowbray's secrets which include motivational quotes and a trip to the video shop.
The player explained: "He reads a lot of books, a lot of people's autobiographies and brings in people's quotes. He'll put some things up on the noticeboard - little captions to make you think about things he obviously thinks about as a manager. He tries to learn from the best. It's a different side of him which he tries to pass on to us.
"I remember, at the start of the season, he showed us a video of the American football film Any Given Sunday. The coach has the players in the dressing-room and he builds them up and motivates them and it gives you a feeling in the stomach that you want to have.
"That was a build-up to the first game and even though we were beaten we all knew what he was meaning and we saw his outlook on the game."
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