Gordon took the flag on his victory lap following win No. 76 on Saturday night at Phoenix International Raceway. His car was pelted with beer cans during the tribute, and fans have been critical of the display in the days since.
But Junior, who congratulated Gordon in victory lane, called the tribute to his father a classy move.
"I don't know how in the world you could take that the wrong way," Earnhardt Jr. said Tuesday during an appearance at Lowe's Motor Speedway. "That's what's bothering me so bad. Jeff can't win for losing.
"He was trying to make a good gesture. That's all that was. I don't think anybody in the world could find anything wrong with what he did. That's a shame he didn't get all the credit he deserved for it."
Gordon's crew decided on the tribute last summer when the driver reached win No. 75. The team had carried the No. 3 flag in its truck ever since.
Aaron Kuehn, a crewman on Gordon's team, approached Junior and his sister at a party last year to get their approval. Earnhardt had forgotten the request until reminded Tuesday.
Earnhardt said he thought his father would have appreciated the moment, and the time the team had to carry the flag before using it.
"That flag rode around in that truck for several months - which my dad would get a real kick about that," he said.
"I don't understand the disrespect - what's the angle there? When you win a race, it's all about you at that moment. You won, you're happy, you're excited, you're the best of the best. "And (Gordon) decided to split that down the middle, 50/50, and give my father some respect and take half of his moment and give it to my dad. I thought that was really classy." Earnhardt took particular issue with fans who threw beer cans onto the track. It's grown increasingly common. And a few years ago it created a dangerous situation at Talladega Superspeedway, where fans showered the track with cans after Gordon beat Earnhardt under caution.
As the Nextel Cup Series heads to Talladega this weekend, Earnhardt acknowledged Gordon could see more animosity - and beer cans - if Gordon wins to break a tie with Dale Earnhardt.
"I'd consider it nasty," he said. "I don't feel comfortable with beer cans flying on the racetrack at any point in time. You see a lot of them are full, half full, hitting people 'cause they're not making it over the fence, knocking people in the back of the head.
"I've seen that happen on occasion. It's a dangerous business. I don't think it's cool. It ain't cool at all."
Earnhardt said it's a misconception that his father and Gordon were bitter rivals, saying the two were friends who partnered together in several business ventures. And when Gordon was breaking into the sport, it was the elder Earnhardt who helped him understand the etiquette of big-time racing. "I never remember a rivalry. ... I actually never remember any problems," Rick Hendrick, Gordon's car owner, said. "I think there was a lot of respect there. I think when you've got two popular drivers, different fan base, I think a lot of times the fans create the rivalry. "I think in that case it was just the Earnhardt fans didn't want to see Jeff win. And Jeff fans against Earnhardt."