Brandon Gormley also scored for the Coyotes (8-9-1) who have put together back-to-back victories after dropping three in a row.
Taylor Hall replied for the Oilers (6-10-2), who have lost three straight and have yet to defeat a Western Conference opponent this season— falling to 0-8-1 in that department. Twenty of Edmonton's next 23 games are against the West.
The best opportunity to start the scoring came with seven-and-a-half minutes remaining in the first period as Oiler centre Ryan Nugent-Hopkins almost had a short-handed breakaway. Coyotes goalie Devan Dubnyk, however, came flying well out of his net to knock the puck away.
Arizona capitalized on the same power play just over a minute later as Gormley unleashed a bullet from the top of the circle through traffic and past Oilers starter Ben Scrivens. It was Gormley's first NHL goal.
Edmonton outshot the Coyotes 15-8 through 20 minutes.
The Coyotes had a glorious chance to pad their lead late in the second period on a two-man advantage after Scrivens was charged with a delay of game penalty, But the Edmonton penalty killers didn't allow them a sniff at the net.
The shots favoured the Oilers 25-16 after the second period, with Arizona blocking 14 shots in the second frame alone.
The Coyotes went up 2-0 with seven minutes left in the third as Edmonton had trouble clearing the zone and Antoine Vermette was able to send it in front to Boedker, who beat Scrivens stick-side for his seventh goal of the season and fourth in two games against the Oilers this year.
Edmonton broke Dubnyk's shutout bid a minute later on the power play as Jordan Eberle put a pass through traffic to Hall out front, and he sent his seventh of the year into the net.
The Oilers had a great chance to tie the game with Justin Schultz looking at an empty net, however Martin Erat got a stick out to deflect the shot and preserve the victory.
Dubnyk stopped 33 shots for the win while Scrivens made 26 saves in defeat.
The Coyotes return home for one game against the Washington Capitals on Tuesday before heading out on the road for three more. The Oilers play the third game of a five-game homestand on Wednesday against the Vancouver Canucks.
Notes: It was the second of five games between the Oilers and Coyotes this season. Arizona won the first encounter 7-4 on Oct. 15… The Coyotes entered the game riding a 14-game point streak against the Oilers, tied for the longest point streak against the same opponent in franchise history. The Coyotes last lost in regulation to Edmonton on Jan. 25, 2011… Hall returned to the Oilers lineup after being out the past six games with a strained knee… The game marked the return of a couple of former Oilers for the first time as Dubnyk, their starting goalie from last season, made his first appearance against Edmonton since being traded from the club last January. Dubnyk came into the game with a 3-0-1 record and fresh off a shutout win over the Canucks. Coyotes forward Sam Gagner, who was dealt over the summer by the Oilers, also played his first game against the team he spent his first seven seasons in the NHL with… Out for Arizona was forward David Moss (upper body). The Oilers were completely healthy for the first time this season… It was Oilers' head coach Dallas Eakins 100th career game behind the bench. His record is 35-54-11.