Authorities said the two packages were connected to four earlier explosions that have occurred in the state throughout March.
Police also said the FedEx center nor a resident of Schertz, Texas, were the intended targets for the package bomb.
Authorities roped off a large area around the shopping center in the Austin enclave of Sunset Valley where the store is situated.
Federal Bureau of Investigation agent Michelle Lee said the explosion happened around 1 a.m.at a FedEx facility in Schertz, which is just northeast of San Antonio and about 60 miles southwest of Austin. She did not have details about the size or weight, or a description of the package.
KENS 5 received a call from one woman whose husband works at the facility. She has since been released. He said that federal law enforcement was already working with local officials to identify the source of the attacks.
"We are investigating it as being possibly related to our open investigation", FBI spokeswoman Michelle Lee told the Austin American-Statesman newspaper.
Police officials have asked the public to be vigilant and report any suspicious packages.
The blast comes as authorities search for answers to a series of explosions that have rattled Austin.
Police and federal agents said Sunday night's blast triggered along a street by a almost invisible tripwire suggests a "higher level of sophistication" than they have seen before in three early package bombs left on doorsteps, and means the carnage is now random, rather than targeted at someone in particular.More news: Dele Alli, the best player for his age in world football?
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"The use of a tripwire is far less discriminating than leaving parcel bombs at residences and suggests that (Sunday's) victims were not specifically targeted", the global think tank Stratfor said in one of its Threat Lens reports.
"Stay inside your home until we have had a chance to deem this neighborhood safe", Manley said at a streetside news conference.
He added that the person responsible for the bombings had previously been "very sophisticated in going around surveillance cameras".
But Manley said Sunday's bombing also seriously wounded two white men aged 22 and 23 as they walked in a quiet residential neighbourhood. On the night of the bombing, one of the victims was riding a bike in the street and the other was on a sidewalk when they crossed a tripwire that he said knocked "them both off their feet".
In the past few days whole communities have been locked down, locals are being told not to touch anything suspicious and even keep an eye where they're walking.
"The similarities they've seen to this point, lead them to believe - as we do - that these are all being constructed by the same person or persons who are responsible for this". "And it blew up".
The individual or people behind the bombings are likely to be highly skilled and methodical, said Fred Burton, chief security officer for Stratfor, a private intelligence and security consulting firm based in Austin.
The president spoke to reporters at the White House about the attacks during a visit with Saudi Arabia's crown prince Mohammed bin Salman.
Officials would not say where the package destination was, and officials would not confirm whether or not this explosion was related to the serial bombings in Austin, or if there were nails and shrapnel in the package.