LA Galaxy striker Ibrahimovic was named in the side for the second successive campaign after scoring 30 goals and assisting seven more in 29 regular-season matches.
Vela has enjoyed a stellar year with Los Angeles FC, meanwhile, having netted a single-season record 34 goals to win the Golden Boot and earn links with a move to LaLiga giants Barcelona.
LAFC won the Supporters' Shield and are well represented, with midfielder Eduard Atuesta and defender Walker Zimmerman also included.
There was also a place for Atlanta United's Josef Martinez, who broke his own MLS record by scoring a goal in 15 consecutive matches this year.
Vito Mannone got the nod in goal after making 129 saves in his debut campaign with Minnesota United, helping them qualify for the MLS Cup Playoffs for the first time.
MLS Best XI: Vito Mannone (Minnesota); Ike Opara (Minnesota), Miles Robinson (Atlanta), Walker Zimmerman (LAFC); Alejandro Pozuelo (Toronto), Carles Gil (New England), Eduard Atuesta (LAFC), Maxi Moralez (NYCFC); Carlos Vela (LAFC), Josef Martinez (Atlanta), Zlatan Ibrahimovic (LA Galaxy).