The flight was also memorable for its dramatic re-entry. The craft's service module did not separate, so it entered the atmosphere nose-first, leaving cosmonaut Boris Volynov hanging by his restraining straps. As the craft aerobraked, the atmosphere burned through the module. But the craft righted itself before the escape hatch was burned through. Then, the parachute lines tangled and the landing rockets failed, resulting in a hard landing which broke Volynov's teeth.

The Soyuz 4 and 5 spacecraft docked on 16 January 1969, the first time two crewed spacecraft had docked (Apollo 9 would do the same in March of the same year). The two craft possessed only a primitive probe (Soyuz 4) and drogue (Soyuz 5) docking assembly. A connecting tunnel for the docking mechanism had not yet been developed, which prevented a simple internal transfer between the craft. This required the two transferring cosmonauts to spacewalk from one vehicle to the other. Aboard Soyuz 5, Yevgeny Khrunov and Aleksei Yeliseyev immediately began preparing for their extravehicular activity (EVA). Boris Volynov, who would remain aboard Soyuz 5, filmed them donning their Yastreb space suits.

On their 35th revolution of Earth, the two cosmonauts exited the spacecraft for the second Soviet spacewalk. One of Khrunov's lines became tangled and he accidentally closed the tumbler of his suit ventilator. This distracted Yeliseyev who did not set up the movie camera on the orbital module before exiting the spacecraft. As such, there is no film of the historic EVA, only a poor video transmission. One hour later, the two were greeted by Shatalov after the repressurisation of the Soyuz 4 orbital module, which also acted as an airlock. Soyuz 4 and 5 separated after 4 hours and 35 minutes docked together. Soyuz 4 re-entered the atmosphere and landed at 100 km (62 mi) at the southwest of Karaganda, in Kazakhstan, on 17 January 1969.

The mission proved it was possible to perform the activities that would be needed on a Soviet lunar landing. The Soviet plan called for a lone cosmonaut to land on the Moon, return to lunar orbit, then make a spacewalk back from the landing craft to the orbiting spacecraft after docking. This was because there was no internal tunnel between the two craft as found on the American Apollo CSM and LM.

The crew were to meet Leonid Brezhnev during a lavish ceremony at the Kremlin, but this was prevented by an attempted assassination of the Soviet leader. A man shot eight times at the motorcade but aimed at the car containing Georgy Beregovoy, Alexei Leonov, Andriyan Nikolayev, and Valentina Tereshkova. They were unharmed but Brezhnev's car was forced to speed away past the waiting Soyuz 4/5 crews on the podium

Soyuz 5 (Russian: Союз 5, Union 5) was a Soyuz mission using the Soyuz 7K-OK spacecraft launched by the Soviet Union on January 15, 1969, which docked with Soyuz 4 in orbit. It was the first-ever docking of two manned spacecraft of any nation, and the first-ever transfer of crew from one space vehicle to another of any nation, the only time a transfer was accomplished with a spacewalk - two month before the US Apollo 9 performed the first ever internal crew transfer.