There were a wide variety of technological innovations over the course of the Civil War, both in terms of new technologies used directly for warfare, and those which would become commercialized. For new weapons, the United States saw the introduction of the repeating rifle, the Minié ball, and the submarine. Inventions and innovations not directly related to the civil war included the telegraph and the railroad.
The repeating rifle was introduced in 1863, 2 years after the start of the war. Previously, soldiers had to pause to reload bullets in between shots, losing valuable time in which the enemy could attack. Now, however, some rifles had the ability to fire as many as 7 shots in 30 seconds (such as the Spencer Carbine). While this may not seem like a lot compared to the technology that we have today, the difference was immense for soldiers.
The Minié ball (named after Claude Minié) replaced the earlier musket ball. The Minié ball moved much faster, and therefore, struck soldiers with much more force. The force with which it struck soldiers was enough to shatter bone upon impact (a reason which amputation became much more used than it had been in earlier wars). This bullet was also much easier to load than the musket balls. Previously, soldiers had to force the bullet in, sometimes using a mallet to pound it in. Again, this wasted valuable time, so the invention of the Minié ball hastened the process.
Combined, the repeating rifle and the Minié ball had a huge impact on how war was fought. Previously, the most range that one could get out of a shot was about 250 yards, with rifles only being accurate within 80 yards, meaning that battling sides were very close to each other. Now, however, the range increased to 1000 yards, pushing the two sides away from each other.
The Civil War saw submarines being used with increasing frequency, particularly in naval battles. These came about due to ironclad warships (another innovation), which were ships made out of sheets or iron sheets joined together. The Union primarily had access to these, and used them to blockade the Confederacy. To combat this technology the Confederacy began to use submarines, which were essentially metal tubes. They worked, however, they often ended up sinking themselves as well.
It is important to remember that while these technologies changed the face of warfare, they were primarily only available to Union troops (with the exceptions being the submarine and the Minié ball).
The telegraph had been invented prior to the Civil War, but became a game changer for communication with troops. Abraham Lincoln was the first president who was able to directly communicate with his troops, without being on the battlefield. He could communicate about casualties, battlefield strategy, and supplies. The Confederacy did not have as advanced of a telegraph system, and was thus unable to utilize this technology to the same extent as the Union.
The railroad was another innovation that was greatly utilized by the Union, but not so much by the Confederacy. At the beginning of the war, the Union had a clear advantage - they had 20,000 miles of tracks, as opposed to the South's 9,000. They also housed many of the nation's locomotive factories, and had standardized the track width - something the Confederacy had not yet done. Because of the difference in the track mileage, the Union had a massive advantage over the confederacy when it came to the transport of ammunition, general supplies, and troops.