Benavides went into Thursday's 456km Riyadh-Al Qaisumah stage third overall and 3m24s off overnight leader Xavier de Soultrait, but only 14th in the running order owing to his finishing position on the previous day's test.
That put in the Argentinian in a good position to fight for the win, as he spent the stage battling his junior Honda colleague and fellow South American Jose Ignacio Cornejo.
Having trailed by five minutes at the 74km mark, Benavides clawed back that time over the remainder of the stage, despite reportedly suffering a crash and injuring his nose just after the 330km mark, finishing exactly one minute clear of Cornejo.
A late surge by KTM man Toby Price left the Australian a strong third, just 20 seconds further back, while Sherco rider Lorenzo Santolino was an impressive fourth ahead of another factory KTM rider, Sam Sunderland.
Husqvarna privateer de Soultrait was sixth on the day, and lost only one place overall to sit just 2m31s behind new leader Benavides in the standings.
Cornejo meanwhile has leapt from ninth to third, 3m42s back, with Price only one second behind the Chilean in fourth and Sunderland completing a tightly-bunched top five.
Wednesday's stage winner Joan Barreda continued the established trend of the rider opening the road suffering as he gave away some 19 minutes to teammate Benavides, losing almost all of that time with an early navigational error.
Having gone into the day only 15s away from the head of the standings, the Spaniard has slipped to ninth, 14m02s away from the lead.
Reigning champion Ricky Brabec's tactic of deliberately slowing on Wednesday's stage to give himself a better road position didn't pay dividends, as he ended up losing 14 minutes to Benavides. He did however gain one position overall, moving up to 14th.
Yamaha rider Adrian van Beveren's hopes of challenging for the podium look to be over after the Frenchman dropped nearly 40 minutes after getting lost early in the stage.
That leaves Ross Branch as the marque's only realistic hope of a top result, with the Botswanan rider holding eighth behind erstwhile leader Skyler Howes (KTM).
Standings after Stage 5 (Top 10):
Xavier de Soultrait
Jose Ignacio Cornejo