Howes, riding for the factory Husqvarna team, briefly lost the lead to compatriot Mason Klein after Stage 8 on Sunday, but was promoted back to the head of the standings when his rival was penalised for speeding.
Klein, the 21-year-old who is contesting only his second Dakar on a privateer KTM, secured his first stage win on the second day of the Saudi Arabian event to announce himself as a potential contender for victory a year on from finishing ninth overall and top rookie in 2022.
A fuel pump failure in the fourth stage and then a pair of crashes on the sixth stage saw Klein slip to seventh overall, but a strong run to second on Sunday’s eighth stage allowed him to temporarily leapfrog overnight leader Howes with a provisional lead of 47 seconds.
However, after Klein's two-minute speeding penalty was applied, Howes moved back into the top spot by 1m13s ahead of both Klein and KTM's Kevin Benavides on identical times with six stages left to run.
There was drama from the very opening stage as defending champion Sam Sunderland, representing KTM sub-brand GasGas, suffered a fall after just 52km and had to be evacuated by helicopter with a broken shoulder and bruising on his back.
It marked the second time Sunderland has crashed out during his title defence, as he failed to make the finish in 2018 following his 2017 triumph for KTM.
Two stages later, Honda man and 2020 Dakar winner Ricky Brabec had a crash of his own and had to withdraw due to neck pain, although he avoided sustaining any fractures.
Daniel Sanders, Sunderland’s GasGas teammate, won the third stage to assume the lead at this point, but dropped down the order after a difficult fifth stage, struggling with illness.
That allowed Howes to grab the advantage, with a new ‘time bonus’ rule for this year’s Dakar leading to fewer fluctuations in the day-to-day classifications by awarding bonus seconds to riders for opening the road in the early part of stage, to be deducted from their final time.
However, Howes, along with Toby Price (KTM) - who had been second overall - and Stage 6 winner Luciano Benavides (Husqvarna) all lost precious ground opening the road on Stage 8.
Two-time champion Price now sits fourth overall, 2m58s down on the lead, ahead of Honda pair Pablo Quintanilla (3m45s down) and Adrien van Beveren (3m49s), who won Stage 5 in his first Dakar representing the brand following the withdrawal of Yamaha.
Sanders sat seventh, 8m03s off the lead, while Joan Barreda was eighth aboard his privately-entered but factory-supported Honda after being replaced in the marque's works line-up by van Beveren.
Barreda has endured an eventful Dakar so far as he continues to chase an elusive first title, fracturing his toe on Stage 2 but riding through the pain to take a landmark 30th stage win two days later to extend his lead in the all-time standings among active riders.
Towards the end of Stage 5, the Spaniard suffered a crash in which his helmet was run over by Price, leading to him briefly losing consciousness - but he opted to continue once he regained his senses, helped by Price, Quintarilla and Howes.
Despite a difficult Stage 8, Barreda remains within 8m21s of the lead, while Jose Ignacio Cornejo (Honda) and another former winner in the form of Mathias Walkner (KTM) complete the top 10, followed by Luciano Benavides in 11th.
Another Yamaha refugee, Ross Branch, took the stage win on Sunday for the Indian Hero brand ahead of Klein. However, the Botswana rider is way down in 35th overall after losing considerable ground in Stage 4 after running out of fuel.
Provisional standings after Stage 8:
| Pos. | Rider | Bike | Time | Penalties |
| 1 |
 Skyler Howes |
Husqvarna | 30h33'16 | |
| 2 |
Mason Klein |
KTM | +1'13 | 4'00 |
| 3 |
 Kevin Benavídes |
KTM | +1'13 | 3'00 |
| 4 |
 Toby Price |
KTM | +2'58 | 1'00 |
| 5 |
 Pablo Quintanilla |
Honda | +3'45 | 2'00 |
| 6 |
 Adrien van Beveren |
Honda | +3'49 | |
| 7 |
Daniel Sanders |
GasGas | +8'03 | 4'00 |
| 8 |
 Joan Barreda |
Honda | +8'21 | 1'00 |
| 9 |
 Jose Ignacio Cornejo |
Honda | +20'32 | |
| 10 |
 Matthias Walkner |
KTM | +23'35 |
