Memphis Depay scored his first United goal as LVG's side secured a second win of Tour 2015 in California on Tuesday night.
The £31m Dutchman's effort- a calm, low, well-taken finish- was sandwiched between strikes from Juan Mata and Andreas Pereira, who also netted his first goal for the senior team.
Van Gaal started with the same team that overcame Club America in Seattle- and his attacking duo of Depay and Rooney were at it from the off.
In the fourth minute, the Dutchman powered forward, twisted and turned before he saw his shot parried by David Bingham in the Quakes goal, and, from the rebound, Mata could only find the side netting.
Five minutes later, a superb Luke Shaw run down the left almost dropped to Depay, but the Quakes managed to clear the ensuing danger.
Rooney again narrowly failed to convert from a good position, before United's pressure told and Mata-somewhat inadvertently- gave us the lead with 32 minutes on the clock.
Picked out by Ashley Young- who impressed throughout on the left-hand side- the Spaniard seemed to be aiming for the onrushing Depay- but the ball evaded everyone and nestled into the corner.
Four minutes later, Depay did manage to get his name on the scoresheet, when he capitalised on a poor backpass and slotted home from close range.
With the half drawing to a close, the MLS side were given a lifeline and halved the deficit through Fatai Alashe, whom steered in a sliding finish from Shea Salinas' run and cut-back.
After Mata had seen an effort well-saved on the stroke of half-time, LVG stuck to his plan of fielding the same XI that had come on at the break in Seattle, although Sam Johnstone remained in goal owing to fitness concerns to both David de Gea and Anders Lindegaard.
There was one slight tactical tweak with Adnan Januzaj moving out to the left to allow Pereira to take up the no.10 position the Belgian had played in the opening tour match.
It was the young Brazilian who restored the Reds two-goal advantage just after the hour mark with a fine header from Jesse Lingard's in swinging cross.
Marc Pelosi lashed an effort just over the bar for the Earthquakes, and Chris Smalling also went close with a header late on, but there were no further chances as United made it two wins from two on the tour.
Next up... Barcelona on Saturday in Santa Clara.
United first half XI: Johnstone; Darmian, Jones, Blind, Shaw; Mata, Carrick, Schneiderlin, Young; Depay; Rooney.
Second half XI: Johnstone; McNair, Smalling, Evans, Blackett; Schweinsteiger, Herrera; Lingard, Pereira, Januzaj; Wilson.