Boulter said she had "dreamt" of playing at a Queen's tournament after she came through a match filled with twists and turns against Tomljanovic.
After years of watching the men's tournament, the 28-year-old said it was "special" to play in the inaugural women's WTA 500 event at the iconic venue.
"I came out yesterday to watch Andy get his first court [named after him], which is special in itself," she said.
"To get the women back here feels very special. It's actually something I dreamt of, having come here the last couple of years to watch the men play, so I'm just really grateful to be on this court."
In her first singles match of the season on the surface, Boulter navigated a tricky hold where she saw off break points before impressively breaking to love, but missed the opportunity at 5-4 to serve out the set.
Instead, Boulter relied on her serve to get her out of trouble in the first-set tie-break, smashing a forehand winner to take the set in just over an hour.
But things spiralled rapidly for Boulter in set two as she struggled to find any rhythm, falling down a double break and struggling to find the answers.
And, having relied so heavily on a strong serve in the first set, she double-faulted on the first point of the opening game in the decider, laying the foundations for Tomljanovic to break.
Now on a run of six games without a win for Boulter, the home crowd was flat and struggled to provide the Briton with the boost she needed.
That came soon after, though, as Boulter immediately broke back and rediscovered some momentum to win three games in a row.
More to-ing and fro-ing followed as neither player could hold their serve but Boulter eventually kept her calm at 4-4, holding serve before taking the match when Tomljanovic's forehand dropped long.
She will face Poland's Magdalena Frech or fifth seed Diana Shnaider in the next round.