It's the 12th career win for Hunter-Reay, who was alone up front during the caution until Andretti pulled even at the finish line to savor the moment with his teammate. He led three times for a total of 40 laps.
"They've given us great cars here, and a second win in a row for Ryan is awesome," said Andretti, whose radio worked only sporadically down the stretch.
Dixon said running a time race was "kind of annoying" and Andretti said it removed some strategy from the formula. They wound up going 69 laps, and Hunter-Reay was up front for the final time starting on No. 52.
"The race should be the full distance," Dixon said. "To have to shorten these races for TV, you know, I understand the difficult predicament that everybody is in, but these are championship races. They all pay the same amount of points.
"You decide to take 30 laps off them ... I think it changes strategy a lot and you're constantly chasing that window. Then ultimately you finish on a caution, too, which is also a bit of a bummer for the fans. In the future, hopefully we can find a way around that."
Drivers were focused on handling the track conditions, not payback from any lingering anger over Long Beach clashes.
It ended badly for Aleshin, who walked back to pit road while the rest of the field finished. Earlier Sebastien Bourdais had spun the Russian from behind, leaving him stalled. Bourdais received a drive-through penalty for avoidable contact.
The race was a change-up for Dixon, who finished second in each of the first four races at Barber.
"We went the wrong way, but it was an interesting day," Dixon said. "Whenever you have a rain delay it sort of puts a strain on everybody trying to figure out what we need to do.
"The cars were pretty good. The track suits wet conditions. There were a few troublesome areas with standing water and a few of the guys found those spots. But generally the race went fairly smoothly."