Matty Russell gave Wolves the perfect start but Joe Mellor's converted score gave Widnes a narrow lead.
Peta Hiku put Warrington back in front before they eased clear through Kevin Brown's score against his former club and a second from Russell.
Both sides will now play in the Qualifiers as they bid to retain their top-flight status for next season.
Huddersfield's win over Leigh Centurions last week meant Warrington, last year's beaten Grand Finalists, knew they would not make the Super 8s this season but they will go into the Qualifiers with confidence after three successive wins.
Widnes, who in contrast have now lost four games in a row, could end up finishing bottom of the regular season table if the Centurions beat Salford on Friday.
The two sides will face each other again in the Qualifiers, with the Wolves having won all three of this season's meetings in Super League and Challenge Cup.
Warrington coach Tony Smith:
"It was a good workout and timely for us. I thought we were a bit rusty the way we were playing in the first half and we were rushing things and trying to throw passes when we didn't need to instead of taking control of the ball and maybe taking the tackle and putting on a better play.
"But we got hold of things in the second half and our defence also got better which enabled to do more with the ball and come up with some good combinations."
Widnes coach Denis Betts:
"Overall I'm disappointed we didn't stay in the fight. You want to win these games and be successful moving forward but you want to respect the process that is going to keep us in Super League which we failed to do in the second half.
"We were patchy again. It was a great 40 minutes and we probably could have asked a few more questions with some of our kicks but we were solid which we haven't been over the last couple of weeks.
"We just failed to apply the pressure when we had the ball in the second half, we dropped the ball twice on their line and gave a penalty away and didn't really get back into the game.
"We now have a two-week break and then have seven games in a mini-season and it gives us the chance to right a couple of wrongs when we feel we have let ourselves down by losing close games."
Warrington: Ratchford, Russell, Hiku, Atkins, Lineham, Patton, Brown, Cooper, Clark, Sims, Jullien, Hughes, Philbin.
Replacements: Currie, G. King, Savelio, Smith.
Widnes: Thompson, Armstrong, Chamberlain, Runciman, Marsh, Mellor, B. Walker, J. Chapelhow, Johnstone, Dudson, Whitley, Olbison, Cahill.
Replacements: Gerrard, Burke, D. Walker, T. Chapelhow.
Referee: Robert Hicks (RFL)
Warrington overturned a half-time deficit to end the regular season Super League campaign with a win over Widnes.