Trailing 2-0 at the break after being second best in the first half, the Head Coach replaced injured Jermaine Jenas and Young-Pyo Lee with striker Darren Bent and midfielder Tom Huddlestone.
Bent was pushed furthest forward with support slightly deeper from Robbie Keane and Dimitar Berbatov, Didier Zokora stepped into the defensive line and both Pascal Chimbonda and Gareth Bale were encouraged to push on down the flanks.
It worked a treat - in fact, within a minute of the restart, when Huddlestone threaded a pass through for Dimitar Berbatov to reduce the deficit to 2-1.
Our tails were up from that point. Steed Malbranque levelled within five minutes and Bent poked home what turned out to be the winner from Aaron Lennon's cross after 66 minutes.
"The credit has to go to the players, who had a fantastic second half," said Juande. "There was a lot of intensity, especially after the disastrous first half.
"Things weren't going well in the first half, we had a heavy scoreline against us and that weighed heavily on the team. It wasn't the fault of any one player - any credit or failure is proportional and not the fault of one player, but the group.
"At half-time we reminded the players that the game lasts for 90 minutes, we had to continue working and that it was possible to turn the negative scoreline around.
"The first two goals came quickly so we had plenty of time to score a third, which thankfully we got and the win leaves us well position in our group."
The win took us to the top of Group G, having played a game more than Anderlecht, who we face next Thursday.
In Thursday night's other group game, Hapoel Tel Aviv surprisingly beat Getafe 2-1 in Spain.
Nothing is decided yet in the group but we are now on six points and in the three seasons of the UEFA Cup's group stage system (and therefore 24 groups played so far) a team gaining six points has only failed to progress on one occasion - Rangers back in 2004-05.
Juande Ramos refused to take the credit after his half-time changes turned the tide against Aalborg on Thursday night.