FortiGate Next Generation Firewall utilizes purpose-built security processors and threat intelligence security services from FortiGuard labs to deliver top-rated protection and high performance, including encrypted traffic.
Article Id 192442
By default, FortiGate will only negotiate and try to bring up Phase2 tunnel when 'interesting' traffic is matched to an IPSec policy.

In situations where an IPSec tunnel is needed to be up already before traffic passes through a policy, auto-negotiation must be enabled under phase2 settings of IPsec VPN tunnel.
Therefore, FortiGate will negotiate and try to bring up Phase2 tunnel automatically.

FortiOS firmware version 4.00 MR3
FortiOS firmware version 5.0.x

This is applicable for any site-to-site IPSec VPN between two FortiGates or another vendor.

Assuming an IPSec VPN connection to 'FortiGate B' or 'Vendor Firewall' has already been configured from 'FortiGate A'. 
If for any reason, the remote FortiGate/firewall unit is rebooted, an administrator may wish to have this IPSec tunnel come back up automatically, meaning before any traffic is initiated.
For this to happen, a CLI Phase 2 setting must be enabled in configuration of all those tunnels, which should automatically recover when necessary and be brought up immediately.
From CLI.
For route based IPSec:
# config vpn ipsec phase2-interface
    edit <name>
        set auto-negotiate enable
For policy based IPSec:
# config vpn ipsec phase2
    edit <name>
        set auto-negotiate enable
It is also possible to enable from GUI:

GUI – VPN – IPsec Tunnels – VPN tunnel name – Phase2 selectors – Advanced – Auto-negotiate.

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Technical Tip: How to configure VPN Site to Site between FortiGates (Using VPN Setup Wizard)