Erdogan also signalled the "readiness" of Turkey's private sector to help Qatar with its multi-billion projects for the 2022 football World Cup, according to the Qatar News Agency.
He held talks with Qatar's Emir Sheikh Tamim bin Hamad al-Thani during the visit, reported QNA.
It also said the two countries signed a number of financial, tourism and research agreements.
"Erdogan stressed the continued support of Turkey to the State of Qatar in various fields, especially in the industrial and military," read the QNA statement.
Turkey has a military base in Qatar, which Ankara says has facilities for around 3,000 troops.
During Wednesday's visit Erdogan visited the Turkish military base with senior Qatari officials, including Defence Minister Khalid bin Mohamed al-Attiyah.
Erdogan's backing came during his second official visit to Qatar, a close ally, since a bitter regional crisis began five months ago, threatening to destabilise the Gulf.
The increasingly entrenched dispute erupted on June 5 when Qatar was politically and economically boycotted by a quartet of neighbouring countries over its alleged support for terrorist groups and relations with Iran.
Qatar, the world's largest exporter of liquified natural gas, denies the charges and says the dispute is an attack on its sovereignty.
Erdogan was in Qatar 24 hours after visiting Kuwait, which has acted as a mediator during the Gulf dispute.
Relations between Turkey and Qatar are exceptionally friendly.
Qatar's Sheikh Tamim was the first foreign leader to phone Erdogan during the unsuccessful Turkish coup in July 2016, according to Turkish state media.
Trade between the two countries at the end of 2015 stood at $1.26 billion.
This is figure is likely to grow, partly because of the Gulf crisis, as Qatar has used Turkey to replace traditional regional food suppliers because of the boycott.
Recent contracts won by Turkish companies in Qatar, include one to build a 10-lane highway.
In 2016, Qatari broadcaster beIN Media announced it had purchased Turkey’s pay TV company Digiturk.
Erdogan left Qatar on Wednesday evening, said QNA.