After taking the first set 6-4 in 55 minutes, the Indian Wells champion found herself up against the wall in the second set against a rampant Vaidisova, who made her WTA comeback this year after retiring in 2010.
Vaidisova broke Halep's serve four times in the second to claim the set 6-2 and force a decider.
Despite her shoddy performance in the second set, Halep bounced back and was just too much for Vaidisova to handle as she went on to win the set and with it the match, 6-4, 2-6, 6-1.
Halep will face Camila Giorgi in the third round after the Italian beat Alison Van Uytvanck 6-3, 6-2.
World number six Ana Ivanovic was also made to toil in her second round match against Irina Falconi before claiming a 7-5, 6 (4)-7, 6-3 triumph.
Despite winning the first set 7-5, Ivanovic failed to take advantage of her 5-2 lead in the second as Falconi, who is ranked 100th, won four of the next five games and saved three match points to force a tie-break, which she duly won.
However, after taking a 3-2 lead in the third set, Ivanovic never looked back as she completed the victory.
Unlike Halep and Ivanovic, two-time Miami Open champion Victoria Azarenka had no problems whatsoever in her second round match against Serbia's Jelena Jankovic.
The clash of the two former world number ones was expected to be a highly intense battle, but Azarenka took the first set 6-1 in just 28 minutes.
Jankovic, who was the runner-up at Indian Wells last week, did put up more of a fight in the second as she forced a 12-deuce game before Azarenka finished her off and won the match 6-1, 6-1 in just under 90 minutes.
Meanwhile, Sabine Lisicki, Svetlana Kuznetsova and Flavia Pennetta all booked their spots in the third round after winning their respective second round matches.