"It was a tough start to the rally with some struggles on Friday, but we worked through that methodically to return stronger. With Dani finishing third, we've picked up a healthy score of points which helps to get us back firmly into the title fight.
"An incredible weekend for us."
Paddon was disappointed to finish sixth but is happy to take away some championship points and look at some positives from the experience.
"Our focus on this final morning was simply on bringing the car home and scoring a few more points," he said.
"It's been a learning weekend for us, but we have to find the positives. Even if the end result doesn't show it, we have been competing closer to the front this weekend and shown an improvement from last year's Tour de Corse. There's obviously still plenty to learn but we're making progress.
"We must now look ahead to the next rally, the start of a run of five on gravel. We should have a good road position for Argentina so I'm looking to feature more prominently in the next events.
"Congratulations to Thierry and Nicolas - and everyone back at Alzenau - for the victory."
Toyota's Jari-Matti Latvala pipped Citroen's Craig Breen for fourth by one tenth of a second.
The WRC moves back to gravel for Rally Argentina later this month - where Paddon will defend his debut WRC victory from a year ago.
Results
1. Thierry Neuville (Hyundai)
2. Sebastien Ogier (Ford) +54.7s
3. Dani Sordo (Hyundai) +56.0s
4. Jari-Matti Latvala (Toyota) +1:09.6s
5. Craig Breen (Citroen) +1:09.7s
6. Hayden Paddon (Hyundai) +2:16.3s
Championship Standings
1. Sebastien Ogier (Ford) 88
2. Jari-Matti Latvala (Toyota) 75
3. Thierry Neuville (Hyundai) 54
4. Ott Tanak (Ford) 48
5. Dani Sordo (Hyundai) 47
6. Craig Breen (Citroen) 33
7. Kris Meeke (Citroen) 27
8. Hayden Paddon (Hyundai) 25
9. Elfyn Evans (Ford) 20
10. Andreas Mikkelsen (Skoda) 12